PyPop: a mature open-source software pipeline for population genomics Article Swipe
Alex K. Lancaster
,
Richard M. Single
,
Steven J. Mack
,
Vanessa Sochat
,
Michael Mariani
,
Gordon Webster
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.3389/fimmu.2024.1378512
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.3389/fimmu.2024.1378512
Python for Population Genomics (PyPop) is a software package that processes genotype and allele data and performs large-scale population genetic analyses on highly polymorphic multi-locus genotype data. In particular, PyPop tests data conformity to Hardy-Weinberg equilibrium expectations, performs Ewens-Watterson tests for selection, estimates haplotype frequencies, measures linkage disequilibrium, and tests significance. Standardized means of performing these tests is key for contemporary studies of evolutionary biology and population genetics, and these tests are central to genetic studies of disease association as well. Here, we present PyPop 1.0.0, a new major release of the package, which implements new features using the more robust infrastructure of GitHub, and is distributed via the industry-standard Python Package Index. New features include implementation of the asymmetric linkage disequilibrium measures and, of particular interest to the immunogenetics research communities, support for modern nomenclature, including colon-delimited allele names, and improvements to meta-analysis features for aggregating outputs for multiple populations. Code available at: https://zenodo.org/records/10080668 and https://github.com/alexlancaster/pypop
Related Topics
Concepts
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.3389/fimmu.2024.1378512
- https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1378512/pdf
- OA Status
- gold
- Cited By
- 6
- References
- 37
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4393431742
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
-
https://openalex.org/W4393431742Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.3389/fimmu.2024.1378512Digital Object Identifier
- Title
-
PyPop: a mature open-source software pipeline for population genomicsWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2024Year of publication
- Publication date
-
2024-04-02Full publication date if available
- Authors
-
Alex K. Lancaster, Richard M. Single, Steven J. Mack, Vanessa Sochat, Michael Mariani, Gordon WebsterList of authors in order
- Landing page
-
https://doi.org/10.3389/fimmu.2024.1378512Publisher landing page
- PDF URL
-
https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1378512/pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1378512/pdfDirect OA link when available
- Concepts
-
Genomics, Open source, Open source software, Pipeline (software), Population genomics, Computational biology, Software, Biology, Population, Computer science, Data science, Genetics, Medicine, Genome, Operating system, Gene, Environmental healthTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
6Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 4, 2024: 2Per-year citation counts (last 5 years)
- References (count)
-
37Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
Full payload
| id | https://openalex.org/W4393431742 |
|---|---|
| doi | https://doi.org/10.3389/fimmu.2024.1378512 |
| ids.doi | https://doi.org/10.5281/zenodo.10799312 |
| ids.pmid | https://pubmed.ncbi.nlm.nih.gov/38629078 |
| ids.openalex | https://openalex.org/W4393431742 |
| fwci | 2.88148335 |
| mesh[0].qualifier_ui | |
| mesh[0].descriptor_ui | D005828 |
| mesh[0].is_major_topic | False |
| mesh[0].qualifier_name | |
| mesh[0].descriptor_name | Genetics, Population |
| mesh[1].qualifier_ui | |
| mesh[1].descriptor_ui | D005838 |
| mesh[1].is_major_topic | False |
| mesh[1].qualifier_name | |
| mesh[1].descriptor_name | Genotype |
| mesh[2].qualifier_ui | |
| mesh[2].descriptor_ui | D006239 |
| mesh[2].is_major_topic | False |
| mesh[2].qualifier_name | |
| mesh[2].descriptor_name | Haplotypes |
| mesh[3].qualifier_ui | |
| mesh[3].descriptor_ui | D056186 |
| mesh[3].is_major_topic | True |
| mesh[3].qualifier_name | |
| mesh[3].descriptor_name | Metagenomics |
| mesh[4].qualifier_ui | |
| mesh[4].descriptor_ui | D012984 |
| mesh[4].is_major_topic | True |
| mesh[4].qualifier_name | |
| mesh[4].descriptor_name | Software |
| mesh[5].qualifier_ui | |
| mesh[5].descriptor_ui | D015201 |
| mesh[5].is_major_topic | False |
| mesh[5].qualifier_name | |
| mesh[5].descriptor_name | Meta-Analysis as Topic |
| mesh[6].qualifier_ui | |
| mesh[6].descriptor_ui | D056186 |
| mesh[6].is_major_topic | True |
| mesh[6].qualifier_name | |
| mesh[6].descriptor_name | Metagenomics |
| mesh[7].qualifier_ui | |
| mesh[7].descriptor_ui | D012984 |
| mesh[7].is_major_topic | True |
| mesh[7].qualifier_name | |
| mesh[7].descriptor_name | Software |
| mesh[8].qualifier_ui | |
| mesh[8].descriptor_ui | D005828 |
| mesh[8].is_major_topic | False |
| mesh[8].qualifier_name | |
| mesh[8].descriptor_name | Genetics, Population |
| mesh[9].qualifier_ui | |
| mesh[9].descriptor_ui | D006239 |
| mesh[9].is_major_topic | False |
| mesh[9].qualifier_name | |
| mesh[9].descriptor_name | Haplotypes |
| mesh[10].qualifier_ui | |
| mesh[10].descriptor_ui | D005838 |
| mesh[10].is_major_topic | False |
| mesh[10].qualifier_name | |
| mesh[10].descriptor_name | Genotype |
| mesh[11].qualifier_ui | |
| mesh[11].descriptor_ui | D005828 |
| mesh[11].is_major_topic | False |
| mesh[11].qualifier_name | |
| mesh[11].descriptor_name | Genetics, Population |
| mesh[12].qualifier_ui | |
| mesh[12].descriptor_ui | D005838 |
| mesh[12].is_major_topic | False |
| mesh[12].qualifier_name | |
| mesh[12].descriptor_name | Genotype |
| mesh[13].qualifier_ui | |
| mesh[13].descriptor_ui | D006239 |
| mesh[13].is_major_topic | False |
| mesh[13].qualifier_name | |
| mesh[13].descriptor_name | Haplotypes |
| mesh[14].qualifier_ui | |
| mesh[14].descriptor_ui | D056186 |
| mesh[14].is_major_topic | True |
| mesh[14].qualifier_name | |
| mesh[14].descriptor_name | Metagenomics |
| mesh[15].qualifier_ui | |
| mesh[15].descriptor_ui | D012984 |
| mesh[15].is_major_topic | True |
| mesh[15].qualifier_name | |
| mesh[15].descriptor_name | Software |
| mesh[16].qualifier_ui | |
| mesh[16].descriptor_ui | D015201 |
| mesh[16].is_major_topic | False |
| mesh[16].qualifier_name | |
| mesh[16].descriptor_name | Meta-Analysis as Topic |
| mesh[17].qualifier_ui | |
| mesh[17].descriptor_ui | D056186 |
| mesh[17].is_major_topic | True |
| mesh[17].qualifier_name | |
| mesh[17].descriptor_name | Metagenomics |
| mesh[18].qualifier_ui | |
| mesh[18].descriptor_ui | D012984 |
| mesh[18].is_major_topic | True |
| mesh[18].qualifier_name | |
| mesh[18].descriptor_name | Software |
| mesh[19].qualifier_ui | |
| mesh[19].descriptor_ui | D005828 |
| mesh[19].is_major_topic | False |
| mesh[19].qualifier_name | |
| mesh[19].descriptor_name | Genetics, Population |
| mesh[20].qualifier_ui | |
| mesh[20].descriptor_ui | D006239 |
| mesh[20].is_major_topic | False |
| mesh[20].qualifier_name | |
| mesh[20].descriptor_name | Haplotypes |
| mesh[21].qualifier_ui | |
| mesh[21].descriptor_ui | D005838 |
| mesh[21].is_major_topic | False |
| mesh[21].qualifier_name | |
| mesh[21].descriptor_name | Genotype |
| mesh[22].qualifier_ui | |
| mesh[22].descriptor_ui | D056186 |
| mesh[22].is_major_topic | True |
| mesh[22].qualifier_name | |
| mesh[22].descriptor_name | Metagenomics |
| mesh[23].qualifier_ui | |
| mesh[23].descriptor_ui | D012984 |
| mesh[23].is_major_topic | True |
| mesh[23].qualifier_name | |
| mesh[23].descriptor_name | Software |
| mesh[24].qualifier_ui | |
| mesh[24].descriptor_ui | D005828 |
| mesh[24].is_major_topic | False |
| mesh[24].qualifier_name | |
| mesh[24].descriptor_name | Genetics, Population |
| mesh[25].qualifier_ui | |
| mesh[25].descriptor_ui | D006239 |
| mesh[25].is_major_topic | False |
| mesh[25].qualifier_name | |
| mesh[25].descriptor_name | Haplotypes |
| mesh[26].qualifier_ui | |
| mesh[26].descriptor_ui | D005838 |
| mesh[26].is_major_topic | False |
| mesh[26].qualifier_name | |
| mesh[26].descriptor_name | Genotype |
| type | article |
| title | PyPop: a mature open-source software pipeline for population genomics |
| awards[0].id | https://openalex.org/G8695514810 |
| awards[0].funder_id | https://openalex.org/F4320337355 |
| awards[0].display_name | |
| awards[0].funder_award_id | R01AI128775 |
| awards[0].funder_display_name | National Institute of Allergy and Infectious Diseases |
| awards[1].id | https://openalex.org/G2794496480 |
| awards[1].funder_id | https://openalex.org/F4320332161 |
| awards[1].display_name | |
| awards[1].funder_award_id | HHSN272201200028C |
| awards[1].funder_display_name | National Institutes of Health |
| awards[2].id | https://openalex.org/G6275209767 |
| awards[2].funder_id | https://openalex.org/F4320337354 |
| awards[2].display_name | |
| awards[2].funder_award_id | R01GM109030 |
| awards[2].funder_display_name | National Institute of General Medical Sciences |
| biblio.issue | |
| biblio.volume | 15 |
| biblio.last_page | 1378512 |
| biblio.first_page | 1378512 |
| topics[0].id | https://openalex.org/T10885 |
| topics[0].field.id | https://openalex.org/fields/13 |
| topics[0].field.display_name | Biochemistry, Genetics and Molecular Biology |
| topics[0].score | 0.9460999965667725 |
| topics[0].domain.id | https://openalex.org/domains/1 |
| topics[0].domain.display_name | Life Sciences |
| topics[0].subfield.id | https://openalex.org/subfields/1312 |
| topics[0].subfield.display_name | Molecular Biology |
| topics[0].display_name | Gene expression and cancer classification |
| topics[1].id | https://openalex.org/T13937 |
| topics[1].field.id | https://openalex.org/fields/13 |
| topics[1].field.display_name | Biochemistry, Genetics and Molecular Biology |
| topics[1].score | 0.9456999897956848 |
| topics[1].domain.id | https://openalex.org/domains/1 |
| topics[1].domain.display_name | Life Sciences |
| topics[1].subfield.id | https://openalex.org/subfields/1312 |
| topics[1].subfield.display_name | Molecular Biology |
| topics[1].display_name | Genetics, Bioinformatics, and Biomedical Research |
| topics[2].id | https://openalex.org/T10887 |
| topics[2].field.id | https://openalex.org/fields/13 |
| topics[2].field.display_name | Biochemistry, Genetics and Molecular Biology |
| topics[2].score | 0.9423999786376953 |
| topics[2].domain.id | https://openalex.org/domains/1 |
| topics[2].domain.display_name | Life Sciences |
| topics[2].subfield.id | https://openalex.org/subfields/1312 |
| topics[2].subfield.display_name | Molecular Biology |
| topics[2].display_name | Bioinformatics and Genomic Networks |
| funders[0].id | https://openalex.org/F4320332161 |
| funders[0].ror | https://ror.org/01cwqze88 |
| funders[0].display_name | National Institutes of Health |
| funders[1].id | https://openalex.org/F4320337354 |
| funders[1].ror | https://ror.org/04q48ey07 |
| funders[1].display_name | National Institute of General Medical Sciences |
| funders[2].id | https://openalex.org/F4320337355 |
| funders[2].ror | https://ror.org/043z4tv69 |
| funders[2].display_name | National Institute of Allergy and Infectious Diseases |
| is_xpac | False |
| apc_list.value | 2950 |
| apc_list.currency | USD |
| apc_list.value_usd | 2950 |
| apc_paid.value | 2950 |
| apc_paid.currency | USD |
| apc_paid.value_usd | 2950 |
| concepts[0].id | https://openalex.org/C189206191 |
| concepts[0].level | 4 |
| concepts[0].score | 0.6708199381828308 |
| concepts[0].wikidata | https://www.wikidata.org/wiki/Q222046 |
| concepts[0].display_name | Genomics |
| concepts[1].id | https://openalex.org/C3018397939 |
| concepts[1].level | 3 |
| concepts[1].score | 0.5872234106063843 |
| concepts[1].wikidata | https://www.wikidata.org/wiki/Q3644502 |
| concepts[1].display_name | Open source |
| concepts[2].id | https://openalex.org/C2988343187 |
| concepts[2].level | 3 |
| concepts[2].score | 0.5652457475662231 |
| concepts[2].wikidata | https://www.wikidata.org/wiki/Q1130645 |
| concepts[2].display_name | Open source software |
| concepts[3].id | https://openalex.org/C43521106 |
| concepts[3].level | 2 |
| concepts[3].score | 0.5497558116912842 |
| concepts[3].wikidata | https://www.wikidata.org/wiki/Q2165493 |
| concepts[3].display_name | Pipeline (software) |
| concepts[4].id | https://openalex.org/C2779040068 |
| concepts[4].level | 5 |
| concepts[4].score | 0.5128993988037109 |
| concepts[4].wikidata | https://www.wikidata.org/wiki/Q7229807 |
| concepts[4].display_name | Population genomics |
| concepts[5].id | https://openalex.org/C70721500 |
| concepts[5].level | 1 |
| concepts[5].score | 0.4450605511665344 |
| concepts[5].wikidata | https://www.wikidata.org/wiki/Q177005 |
| concepts[5].display_name | Computational biology |
| concepts[6].id | https://openalex.org/C2777904410 |
| concepts[6].level | 2 |
| concepts[6].score | 0.4443405866622925 |
| concepts[6].wikidata | https://www.wikidata.org/wiki/Q7397 |
| concepts[6].display_name | Software |
| concepts[7].id | https://openalex.org/C86803240 |
| concepts[7].level | 0 |
| concepts[7].score | 0.4177103042602539 |
| concepts[7].wikidata | https://www.wikidata.org/wiki/Q420 |
| concepts[7].display_name | Biology |
| concepts[8].id | https://openalex.org/C2908647359 |
| concepts[8].level | 2 |
| concepts[8].score | 0.41625431180000305 |
| concepts[8].wikidata | https://www.wikidata.org/wiki/Q2625603 |
| concepts[8].display_name | Population |
| concepts[9].id | https://openalex.org/C41008148 |
| concepts[9].level | 0 |
| concepts[9].score | 0.3967333436012268 |
| concepts[9].wikidata | https://www.wikidata.org/wiki/Q21198 |
| concepts[9].display_name | Computer science |
| concepts[10].id | https://openalex.org/C2522767166 |
| concepts[10].level | 1 |
| concepts[10].score | 0.38355380296707153 |
| concepts[10].wikidata | https://www.wikidata.org/wiki/Q2374463 |
| concepts[10].display_name | Data science |
| concepts[11].id | https://openalex.org/C54355233 |
| concepts[11].level | 1 |
| concepts[11].score | 0.22810345888137817 |
| concepts[11].wikidata | https://www.wikidata.org/wiki/Q7162 |
| concepts[11].display_name | Genetics |
| concepts[12].id | https://openalex.org/C71924100 |
| concepts[12].level | 0 |
| concepts[12].score | 0.21324002742767334 |
| concepts[12].wikidata | https://www.wikidata.org/wiki/Q11190 |
| concepts[12].display_name | Medicine |
| concepts[13].id | https://openalex.org/C141231307 |
| concepts[13].level | 3 |
| concepts[13].score | 0.1919095814228058 |
| concepts[13].wikidata | https://www.wikidata.org/wiki/Q7020 |
| concepts[13].display_name | Genome |
| concepts[14].id | https://openalex.org/C111919701 |
| concepts[14].level | 1 |
| concepts[14].score | 0.12224194407463074 |
| concepts[14].wikidata | https://www.wikidata.org/wiki/Q9135 |
| concepts[14].display_name | Operating system |
| concepts[15].id | https://openalex.org/C104317684 |
| concepts[15].level | 2 |
| concepts[15].score | 0.10228604078292847 |
| concepts[15].wikidata | https://www.wikidata.org/wiki/Q7187 |
| concepts[15].display_name | Gene |
| concepts[16].id | https://openalex.org/C99454951 |
| concepts[16].level | 1 |
| concepts[16].score | 0.0 |
| concepts[16].wikidata | https://www.wikidata.org/wiki/Q932068 |
| concepts[16].display_name | Environmental health |
| keywords[0].id | https://openalex.org/keywords/genomics |
| keywords[0].score | 0.6708199381828308 |
| keywords[0].display_name | Genomics |
| keywords[1].id | https://openalex.org/keywords/open-source |
| keywords[1].score | 0.5872234106063843 |
| keywords[1].display_name | Open source |
| keywords[2].id | https://openalex.org/keywords/open-source-software |
| keywords[2].score | 0.5652457475662231 |
| keywords[2].display_name | Open source software |
| keywords[3].id | https://openalex.org/keywords/pipeline |
| keywords[3].score | 0.5497558116912842 |
| keywords[3].display_name | Pipeline (software) |
| keywords[4].id | https://openalex.org/keywords/population-genomics |
| keywords[4].score | 0.5128993988037109 |
| keywords[4].display_name | Population genomics |
| keywords[5].id | https://openalex.org/keywords/computational-biology |
| keywords[5].score | 0.4450605511665344 |
| keywords[5].display_name | Computational biology |
| keywords[6].id | https://openalex.org/keywords/software |
| keywords[6].score | 0.4443405866622925 |
| keywords[6].display_name | Software |
| keywords[7].id | https://openalex.org/keywords/biology |
| keywords[7].score | 0.4177103042602539 |
| keywords[7].display_name | Biology |
| keywords[8].id | https://openalex.org/keywords/population |
| keywords[8].score | 0.41625431180000305 |
| keywords[8].display_name | Population |
| keywords[9].id | https://openalex.org/keywords/computer-science |
| keywords[9].score | 0.3967333436012268 |
| keywords[9].display_name | Computer science |
| keywords[10].id | https://openalex.org/keywords/data-science |
| keywords[10].score | 0.38355380296707153 |
| keywords[10].display_name | Data science |
| keywords[11].id | https://openalex.org/keywords/genetics |
| keywords[11].score | 0.22810345888137817 |
| keywords[11].display_name | Genetics |
| keywords[12].id | https://openalex.org/keywords/medicine |
| keywords[12].score | 0.21324002742767334 |
| keywords[12].display_name | Medicine |
| keywords[13].id | https://openalex.org/keywords/genome |
| keywords[13].score | 0.1919095814228058 |
| keywords[13].display_name | Genome |
| keywords[14].id | https://openalex.org/keywords/operating-system |
| keywords[14].score | 0.12224194407463074 |
| keywords[14].display_name | Operating system |
| keywords[15].id | https://openalex.org/keywords/gene |
| keywords[15].score | 0.10228604078292847 |
| keywords[15].display_name | Gene |
| language | en |
| locations[0].id | doi:10.3389/fimmu.2024.1378512 |
| locations[0].is_oa | True |
| locations[0].source.id | https://openalex.org/S2595292759 |
| locations[0].source.issn | 1664-3224 |
| locations[0].source.type | journal |
| locations[0].source.is_oa | True |
| locations[0].source.issn_l | 1664-3224 |
| locations[0].source.is_core | True |
| locations[0].source.is_in_doaj | True |
| locations[0].source.display_name | Frontiers in Immunology |
| locations[0].source.host_organization | https://openalex.org/P4310320527 |
| locations[0].source.host_organization_name | Frontiers Media |
| locations[0].source.host_organization_lineage | https://openalex.org/P4310320527 |
| locations[0].source.host_organization_lineage_names | Frontiers Media |
| locations[0].license | cc-by |
| locations[0].pdf_url | https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1378512/pdf |
| locations[0].version | publishedVersion |
| locations[0].raw_type | journal-article |
| locations[0].license_id | https://openalex.org/licenses/cc-by |
| locations[0].is_accepted | True |
| locations[0].is_published | True |
| locations[0].raw_source_name | Frontiers in Immunology |
| locations[0].landing_page_url | https://doi.org/10.3389/fimmu.2024.1378512 |
| locations[1].id | pmid:38629078 |
| locations[1].is_oa | False |
| locations[1].source.id | https://openalex.org/S4306525036 |
| locations[1].source.issn | |
| locations[1].source.type | repository |
| locations[1].source.is_oa | False |
| locations[1].source.issn_l | |
| locations[1].source.is_core | False |
| locations[1].source.is_in_doaj | False |
| locations[1].source.display_name | PubMed |
| locations[1].source.host_organization | https://openalex.org/I1299303238 |
| locations[1].source.host_organization_name | National Institutes of Health |
| locations[1].source.host_organization_lineage | https://openalex.org/I1299303238 |
| locations[1].license | |
| locations[1].pdf_url | |
| locations[1].version | publishedVersion |
| locations[1].raw_type | |
| locations[1].license_id | |
| locations[1].is_accepted | True |
| locations[1].is_published | True |
| locations[1].raw_source_name | Frontiers in immunology |
| locations[1].landing_page_url | https://pubmed.ncbi.nlm.nih.gov/38629078 |
| locations[2].id | pmh:oai:doaj.org/article:be39c84a44ef4727a564110bf1bb8b67 |
| locations[2].is_oa | False |
| locations[2].source.id | https://openalex.org/S4306401280 |
| locations[2].source.issn | |
| locations[2].source.type | repository |
| locations[2].source.is_oa | False |
| locations[2].source.issn_l | |
| locations[2].source.is_core | False |
| locations[2].source.is_in_doaj | False |
| locations[2].source.display_name | DOAJ (DOAJ: Directory of Open Access Journals) |
| locations[2].source.host_organization | |
| locations[2].source.host_organization_name | |
| locations[2].license | |
| locations[2].pdf_url | |
| locations[2].version | submittedVersion |
| locations[2].raw_type | article |
| locations[2].license_id | |
| locations[2].is_accepted | False |
| locations[2].is_published | False |
| locations[2].raw_source_name | Frontiers in Immunology, Vol 15 (2024) |
| locations[2].landing_page_url | https://doaj.org/article/be39c84a44ef4727a564110bf1bb8b67 |
| locations[3].id | pmh:oai:escholarship.org:ark:/13030/qt7mv5v471 |
| locations[3].is_oa | True |
| locations[3].source | |
| locations[3].license | cc-by |
| locations[3].pdf_url | |
| locations[3].version | submittedVersion |
| locations[3].raw_type | article |
| locations[3].license_id | https://openalex.org/licenses/cc-by |
| locations[3].is_accepted | False |
| locations[3].is_published | False |
| locations[3].raw_source_name | |
| locations[3].landing_page_url | https://escholarship.org/uc/item/7mv5v471 |
| locations[4].id | pmh:oai:osti.gov:2471181 |
| locations[4].is_oa | True |
| locations[4].source.id | https://openalex.org/S4306402487 |
| locations[4].source.issn | |
| locations[4].source.type | repository |
| locations[4].source.is_oa | False |
| locations[4].source.issn_l | |
| locations[4].source.is_core | False |
| locations[4].source.is_in_doaj | False |
| locations[4].source.display_name | OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) |
| locations[4].source.host_organization | https://openalex.org/I139351228 |
| locations[4].source.host_organization_name | Office of Scientific and Technical Information |
| locations[4].source.host_organization_lineage | https://openalex.org/I139351228 |
| locations[4].license | cc-by |
| locations[4].pdf_url | |
| locations[4].version | submittedVersion |
| locations[4].raw_type | |
| locations[4].license_id | https://openalex.org/licenses/cc-by |
| locations[4].is_accepted | False |
| locations[4].is_published | False |
| locations[4].raw_source_name | |
| locations[4].landing_page_url | https://www.osti.gov/biblio/2471181 |
| locations[5].id | pmh:oai:pubmedcentral.nih.gov:11019567 |
| locations[5].is_oa | True |
| locations[5].source.id | https://openalex.org/S2764455111 |
| locations[5].source.issn | |
| locations[5].source.type | repository |
| locations[5].source.is_oa | False |
| locations[5].source.issn_l | |
| locations[5].source.is_core | False |
| locations[5].source.is_in_doaj | False |
| locations[5].source.display_name | PubMed Central |
| locations[5].source.host_organization | https://openalex.org/I1299303238 |
| locations[5].source.host_organization_name | National Institutes of Health |
| locations[5].source.host_organization_lineage | https://openalex.org/I1299303238 |
| locations[5].license | other-oa |
| locations[5].pdf_url | |
| locations[5].version | submittedVersion |
| locations[5].raw_type | Text |
| locations[5].license_id | https://openalex.org/licenses/other-oa |
| locations[5].is_accepted | False |
| locations[5].is_published | False |
| locations[5].raw_source_name | Front Immunol |
| locations[5].landing_page_url | https://www.ncbi.nlm.nih.gov/pmc/articles/11019567 |
| locations[6].id | doi:10.5281/zenodo.10602940 |
| locations[6].is_oa | True |
| locations[6].source.id | https://openalex.org/S4306400562 |
| locations[6].source.issn | |
| locations[6].source.type | repository |
| locations[6].source.is_oa | True |
| locations[6].source.issn_l | |
| locations[6].source.is_core | False |
| locations[6].source.is_in_doaj | False |
| locations[6].source.display_name | Zenodo (CERN European Organization for Nuclear Research) |
| locations[6].source.host_organization | https://openalex.org/I67311998 |
| locations[6].source.host_organization_name | European Organization for Nuclear Research |
| locations[6].source.host_organization_lineage | https://openalex.org/I67311998 |
| locations[6].license | |
| locations[6].pdf_url | |
| locations[6].version | |
| locations[6].raw_type | article |
| locations[6].license_id | |
| locations[6].is_accepted | False |
| locations[6].is_published | |
| locations[6].raw_source_name | |
| locations[6].landing_page_url | https://doi.org/10.5281/zenodo.10602940 |
| locations[7].id | doi:10.5281/zenodo.10799312 |
| locations[7].is_oa | True |
| locations[7].source.id | https://openalex.org/S4306400562 |
| locations[7].source.issn | |
| locations[7].source.type | repository |
| locations[7].source.is_oa | True |
| locations[7].source.issn_l | |
| locations[7].source.is_core | False |
| locations[7].source.is_in_doaj | False |
| locations[7].source.display_name | Zenodo (CERN European Organization for Nuclear Research) |
| locations[7].source.host_organization | https://openalex.org/I67311998 |
| locations[7].source.host_organization_name | European Organization for Nuclear Research |
| locations[7].source.host_organization_lineage | https://openalex.org/I67311998 |
| locations[7].license | |
| locations[7].pdf_url | |
| locations[7].version | |
| locations[7].raw_type | article |
| locations[7].license_id | |
| locations[7].is_accepted | False |
| locations[7].is_published | |
| locations[7].raw_source_name | |
| locations[7].landing_page_url | https://doi.org/10.5281/zenodo.10799312 |
| indexed_in | crossref, datacite, doaj, pubmed |
| authorships[0].author.id | https://openalex.org/A5041658734 |
| authorships[0].author.orcid | https://orcid.org/0000-0002-0002-9263 |
| authorships[0].author.display_name | Alex K. Lancaster |
| authorships[0].countries | US |
| authorships[0].affiliations[0].raw_affiliation_string | Institute for Globally Distributed Open Research and Education (IGDORE), Cambridge, MA, United States |
| authorships[0].affiliations[1].raw_affiliation_string | Amber Biology LLC, Cambridge, MA, United States |
| authorships[0].affiliations[2].institution_ids | https://openalex.org/I4210147267 |
| authorships[0].affiliations[2].raw_affiliation_string | Ronin Institute, Montclair, NJ, United States |
| authorships[0].institutions[0].id | https://openalex.org/I4210147267 |
| authorships[0].institutions[0].ror | https://ror.org/04awze035 |
| authorships[0].institutions[0].type | nonprofit |
| authorships[0].institutions[0].lineage | https://openalex.org/I4210147267 |
| authorships[0].institutions[0].country_code | US |
| authorships[0].institutions[0].display_name | Ronin Institute |
| authorships[0].author_position | first |
| authorships[0].raw_author_name | Alexander K. Lancaster |
| authorships[0].is_corresponding | True |
| authorships[0].raw_affiliation_strings | Amber Biology LLC, Cambridge, MA, United States, Institute for Globally Distributed Open Research and Education (IGDORE), Cambridge, MA, United States, Ronin Institute, Montclair, NJ, United States |
| authorships[1].author.id | https://openalex.org/A5024849718 |
| authorships[1].author.orcid | https://orcid.org/0000-0001-6054-6505 |
| authorships[1].author.display_name | Richard M. Single |
| authorships[1].countries | US |
| authorships[1].affiliations[0].institution_ids | https://openalex.org/I111236770 |
| authorships[1].affiliations[0].raw_affiliation_string | Department of Mathematics and Statistics, University of Vermont, Burlington, VT, United States |
| authorships[1].institutions[0].id | https://openalex.org/I111236770 |
| authorships[1].institutions[0].ror | https://ror.org/0155zta11 |
| authorships[1].institutions[0].type | education |
| authorships[1].institutions[0].lineage | https://openalex.org/I111236770 |
| authorships[1].institutions[0].country_code | US |
| authorships[1].institutions[0].display_name | University of Vermont |
| authorships[1].author_position | middle |
| authorships[1].raw_author_name | Richard M. Single |
| authorships[1].is_corresponding | True |
| authorships[1].raw_affiliation_strings | Department of Mathematics and Statistics, University of Vermont, Burlington, VT, United States |
| authorships[2].author.id | https://openalex.org/A5003582043 |
| authorships[2].author.orcid | https://orcid.org/0000-0001-9820-9547 |
| authorships[2].author.display_name | Steven J. Mack |
| authorships[2].countries | US |
| authorships[2].affiliations[0].institution_ids | https://openalex.org/I180670191 |
| authorships[2].affiliations[0].raw_affiliation_string | Department of Pediatrics, University of California, San Francisco, Oakland, CA, United States |
| authorships[2].institutions[0].id | https://openalex.org/I180670191 |
| authorships[2].institutions[0].ror | https://ror.org/043mz5j54 |
| authorships[2].institutions[0].type | education |
| authorships[2].institutions[0].lineage | https://openalex.org/I180670191 |
| authorships[2].institutions[0].country_code | US |
| authorships[2].institutions[0].display_name | University of California, San Francisco |
| authorships[2].author_position | middle |
| authorships[2].raw_author_name | Steven J. Mack |
| authorships[2].is_corresponding | True |
| authorships[2].raw_affiliation_strings | Department of Pediatrics, University of California, San Francisco, Oakland, CA, United States |
| authorships[3].author.id | https://openalex.org/A5088788949 |
| authorships[3].author.orcid | https://orcid.org/0000-0002-4387-3819 |
| authorships[3].author.display_name | Vanessa Sochat |
| authorships[3].countries | US |
| authorships[3].affiliations[0].institution_ids | https://openalex.org/I1282311441 |
| authorships[3].affiliations[0].raw_affiliation_string | Livermore Computing, Lawrence Livermore National Laboratory, Livermore, CA, United States |
| authorships[3].institutions[0].id | https://openalex.org/I1282311441 |
| authorships[3].institutions[0].ror | https://ror.org/041nk4h53 |
| authorships[3].institutions[0].type | facility |
| authorships[3].institutions[0].lineage | https://openalex.org/I1282311441, https://openalex.org/I1330989302, https://openalex.org/I198811213, https://openalex.org/I4210138311 |
| authorships[3].institutions[0].country_code | US |
| authorships[3].institutions[0].display_name | Lawrence Livermore National Laboratory |
| authorships[3].author_position | middle |
| authorships[3].raw_author_name | Vanessa Sochat |
| authorships[3].is_corresponding | False |
| authorships[3].raw_affiliation_strings | Livermore Computing, Lawrence Livermore National Laboratory, Livermore, CA, United States |
| authorships[4].author.id | https://openalex.org/A5073340513 |
| authorships[4].author.orcid | https://orcid.org/0000-0001-5852-0517 |
| authorships[4].author.display_name | Michael Mariani |
| authorships[4].countries | US |
| authorships[4].affiliations[0].raw_affiliation_string | Mariani Systems LLC, Hanover, NH, United States |
| authorships[4].affiliations[1].institution_ids | https://openalex.org/I111236770 |
| authorships[4].affiliations[1].raw_affiliation_string | Department of Mathematics and Statistics, University of Vermont, Burlington, VT, United States |
| authorships[4].institutions[0].id | https://openalex.org/I111236770 |
| authorships[4].institutions[0].ror | https://ror.org/0155zta11 |
| authorships[4].institutions[0].type | education |
| authorships[4].institutions[0].lineage | https://openalex.org/I111236770 |
| authorships[4].institutions[0].country_code | US |
| authorships[4].institutions[0].display_name | University of Vermont |
| authorships[4].author_position | middle |
| authorships[4].raw_author_name | Michael P. Mariani |
| authorships[4].is_corresponding | False |
| authorships[4].raw_affiliation_strings | Department of Mathematics and Statistics, University of Vermont, Burlington, VT, United States, Mariani Systems LLC, Hanover, NH, United States |
| authorships[5].author.id | https://openalex.org/A5005994721 |
| authorships[5].author.orcid | https://orcid.org/0009-0009-2862-0467 |
| authorships[5].author.display_name | Gordon Webster |
| authorships[5].countries | US |
| authorships[5].affiliations[0].raw_affiliation_string | Amber Biology LLC, Cambridge, MA, United States |
| authorships[5].affiliations[1].institution_ids | https://openalex.org/I4210147267 |
| authorships[5].affiliations[1].raw_affiliation_string | Ronin Institute, Montclair, NJ, United States |
| authorships[5].institutions[0].id | https://openalex.org/I4210147267 |
| authorships[5].institutions[0].ror | https://ror.org/04awze035 |
| authorships[5].institutions[0].type | nonprofit |
| authorships[5].institutions[0].lineage | https://openalex.org/I4210147267 |
| authorships[5].institutions[0].country_code | US |
| authorships[5].institutions[0].display_name | Ronin Institute |
| authorships[5].author_position | last |
| authorships[5].raw_author_name | Gordon D. Webster |
| authorships[5].is_corresponding | False |
| authorships[5].raw_affiliation_strings | Amber Biology LLC, Cambridge, MA, United States, Ronin Institute, Montclair, NJ, United States |
| has_content.pdf | True |
| has_content.grobid_xml | False |
| is_paratext | False |
| open_access.is_oa | True |
| open_access.oa_url | https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1378512/pdf |
| open_access.oa_status | gold |
| open_access.any_repository_has_fulltext | False |
| created_date | 2025-10-10T00:00:00 |
| display_name | PyPop: a mature open-source software pipeline for population genomics |
| has_fulltext | False |
| is_retracted | False |
| updated_date | 2025-11-06T06:51:31.235846 |
| primary_topic.id | https://openalex.org/T10885 |
| primary_topic.field.id | https://openalex.org/fields/13 |
| primary_topic.field.display_name | Biochemistry, Genetics and Molecular Biology |
| primary_topic.score | 0.9460999965667725 |
| primary_topic.domain.id | https://openalex.org/domains/1 |
| primary_topic.domain.display_name | Life Sciences |
| primary_topic.subfield.id | https://openalex.org/subfields/1312 |
| primary_topic.subfield.display_name | Molecular Biology |
| primary_topic.display_name | Gene expression and cancer classification |
| related_works | https://openalex.org/W4376877853, https://openalex.org/W1595358351, https://openalex.org/W1493891899, https://openalex.org/W4250928611, https://openalex.org/W166480398, https://openalex.org/W2939866924, https://openalex.org/W1612808768, https://openalex.org/W167327709, https://openalex.org/W1977393088, https://openalex.org/W4233657210 |
| cited_by_count | 6 |
| counts_by_year[0].year | 2025 |
| counts_by_year[0].cited_by_count | 4 |
| counts_by_year[1].year | 2024 |
| counts_by_year[1].cited_by_count | 2 |
| locations_count | 8 |
| best_oa_location.id | doi:10.3389/fimmu.2024.1378512 |
| best_oa_location.is_oa | True |
| best_oa_location.source.id | https://openalex.org/S2595292759 |
| best_oa_location.source.issn | 1664-3224 |
| best_oa_location.source.type | journal |
| best_oa_location.source.is_oa | True |
| best_oa_location.source.issn_l | 1664-3224 |
| best_oa_location.source.is_core | True |
| best_oa_location.source.is_in_doaj | True |
| best_oa_location.source.display_name | Frontiers in Immunology |
| best_oa_location.source.host_organization | https://openalex.org/P4310320527 |
| best_oa_location.source.host_organization_name | Frontiers Media |
| best_oa_location.source.host_organization_lineage | https://openalex.org/P4310320527 |
| best_oa_location.source.host_organization_lineage_names | Frontiers Media |
| best_oa_location.license | cc-by |
| best_oa_location.pdf_url | https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1378512/pdf |
| best_oa_location.version | publishedVersion |
| best_oa_location.raw_type | journal-article |
| best_oa_location.license_id | https://openalex.org/licenses/cc-by |
| best_oa_location.is_accepted | True |
| best_oa_location.is_published | True |
| best_oa_location.raw_source_name | Frontiers in Immunology |
| best_oa_location.landing_page_url | https://doi.org/10.3389/fimmu.2024.1378512 |
| primary_location.id | doi:10.3389/fimmu.2024.1378512 |
| primary_location.is_oa | True |
| primary_location.source.id | https://openalex.org/S2595292759 |
| primary_location.source.issn | 1664-3224 |
| primary_location.source.type | journal |
| primary_location.source.is_oa | True |
| primary_location.source.issn_l | 1664-3224 |
| primary_location.source.is_core | True |
| primary_location.source.is_in_doaj | True |
| primary_location.source.display_name | Frontiers in Immunology |
| primary_location.source.host_organization | https://openalex.org/P4310320527 |
| primary_location.source.host_organization_name | Frontiers Media |
| primary_location.source.host_organization_lineage | https://openalex.org/P4310320527 |
| primary_location.source.host_organization_lineage_names | Frontiers Media |
| primary_location.license | cc-by |
| primary_location.pdf_url | https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1378512/pdf |
| primary_location.version | publishedVersion |
| primary_location.raw_type | journal-article |
| primary_location.license_id | https://openalex.org/licenses/cc-by |
| primary_location.is_accepted | True |
| primary_location.is_published | True |
| primary_location.raw_source_name | Frontiers in Immunology |
| primary_location.landing_page_url | https://doi.org/10.3389/fimmu.2024.1378512 |
| publication_date | 2024-04-02 |
| publication_year | 2024 |
| referenced_works | https://openalex.org/W1952912025, https://openalex.org/W1922272507, https://openalex.org/W1430512513, https://openalex.org/W2020102511, https://openalex.org/W4246535589, https://openalex.org/W2097403532, https://openalex.org/W6670464571, https://openalex.org/W2150999655, https://openalex.org/W2472620693, https://openalex.org/W2161109832, https://openalex.org/W2914196026, https://openalex.org/W2941114381, https://openalex.org/W2100005534, https://openalex.org/W1826574233, https://openalex.org/W2941254773, https://openalex.org/W3147289935, https://openalex.org/W4313626668, https://openalex.org/W2782282960, https://openalex.org/W2923733843, https://openalex.org/W3021633114, https://openalex.org/W2162495518, https://openalex.org/W1491581049, https://openalex.org/W4379769455, https://openalex.org/W2162288649, https://openalex.org/W2114041730, https://openalex.org/W2074776738, https://openalex.org/W2073822313, https://openalex.org/W2140179951, https://openalex.org/W2951354590, https://openalex.org/W2613409207, https://openalex.org/W6969173046, https://openalex.org/W2463568293, https://openalex.org/W6892391608, https://openalex.org/W6911420042, https://openalex.org/W2080237200, https://openalex.org/W4255783720, https://openalex.org/W4393431742 |
| referenced_works_count | 37 |
| abstract_inverted_index.a | 6, 86 |
| abstract_inverted_index.In | 27 |
| abstract_inverted_index.as | 79 |
| abstract_inverted_index.is | 5, 57, 105 |
| abstract_inverted_index.of | 53, 62, 76, 90, 102, 117, 124 |
| abstract_inverted_index.on | 21 |
| abstract_inverted_index.to | 33, 73, 127, 142 |
| abstract_inverted_index.we | 82 |
| abstract_inverted_index.New | 113 |
| abstract_inverted_index.and | 12, 15, 48, 65, 68, 104, 140, 155 |
| abstract_inverted_index.are | 71 |
| abstract_inverted_index.at: | 153 |
| abstract_inverted_index.for | 1, 40, 59, 133, 145, 148 |
| abstract_inverted_index.key | 58 |
| abstract_inverted_index.new | 87, 95 |
| abstract_inverted_index.the | 91, 98, 108, 118, 128 |
| abstract_inverted_index.via | 107 |
| abstract_inverted_index.Code | 151 |
| abstract_inverted_index.and, | 123 |
| abstract_inverted_index.data | 14, 31 |
| abstract_inverted_index.more | 99 |
| abstract_inverted_index.that | 9 |
| abstract_inverted_index.Here, | 81 |
| abstract_inverted_index.PyPop | 29, 84 |
| abstract_inverted_index.data. | 26 |
| abstract_inverted_index.major | 88 |
| abstract_inverted_index.means | 52 |
| abstract_inverted_index.tests | 30, 39, 49, 56, 70 |
| abstract_inverted_index.these | 55, 69 |
| abstract_inverted_index.using | 97 |
| abstract_inverted_index.well. | 80 |
| abstract_inverted_index.which | 93 |
| abstract_inverted_index.1.0.0, | 85 |
| abstract_inverted_index.Index. | 112 |
| abstract_inverted_index.Python | 0, 110 |
| abstract_inverted_index.allele | 13, 138 |
| abstract_inverted_index.highly | 22 |
| abstract_inverted_index.modern | 134 |
| abstract_inverted_index.names, | 139 |
| abstract_inverted_index.robust | 100 |
| abstract_inverted_index.(PyPop) | 4 |
| abstract_inverted_index.GitHub, | 103 |
| abstract_inverted_index.Package | 111 |
| abstract_inverted_index.biology | 64 |
| abstract_inverted_index.central | 72 |
| abstract_inverted_index.disease | 77 |
| abstract_inverted_index.genetic | 19, 74 |
| abstract_inverted_index.include | 115 |
| abstract_inverted_index.linkage | 46, 120 |
| abstract_inverted_index.outputs | 147 |
| abstract_inverted_index.package | 8 |
| abstract_inverted_index.present | 83 |
| abstract_inverted_index.release | 89 |
| abstract_inverted_index.studies | 61, 75 |
| abstract_inverted_index.support | 132 |
| abstract_inverted_index.Genomics | 3 |
| abstract_inverted_index.analyses | 20 |
| abstract_inverted_index.features | 96, 114, 144 |
| abstract_inverted_index.genotype | 11, 25 |
| abstract_inverted_index.interest | 126 |
| abstract_inverted_index.measures | 45, 122 |
| abstract_inverted_index.multiple | 149 |
| abstract_inverted_index.package, | 92 |
| abstract_inverted_index.performs | 16, 37 |
| abstract_inverted_index.research | 130 |
| abstract_inverted_index.software | 7 |
| abstract_inverted_index.available | 152 |
| abstract_inverted_index.estimates | 42 |
| abstract_inverted_index.genetics, | 67 |
| abstract_inverted_index.haplotype | 43 |
| abstract_inverted_index.including | 136 |
| abstract_inverted_index.processes | 10 |
| abstract_inverted_index.Population | 2 |
| abstract_inverted_index.asymmetric | 119 |
| abstract_inverted_index.conformity | 32 |
| abstract_inverted_index.implements | 94 |
| abstract_inverted_index.particular | 125 |
| abstract_inverted_index.performing | 54 |
| abstract_inverted_index.population | 18, 66 |
| abstract_inverted_index.selection, | 41 |
| abstract_inverted_index.aggregating | 146 |
| abstract_inverted_index.association | 78 |
| abstract_inverted_index.distributed | 106 |
| abstract_inverted_index.equilibrium | 35 |
| abstract_inverted_index.large-scale | 17 |
| abstract_inverted_index.multi-locus | 24 |
| abstract_inverted_index.particular, | 28 |
| abstract_inverted_index.polymorphic | 23 |
| abstract_inverted_index.Standardized | 51 |
| abstract_inverted_index.communities, | 131 |
| abstract_inverted_index.contemporary | 60 |
| abstract_inverted_index.evolutionary | 63 |
| abstract_inverted_index.frequencies, | 44 |
| abstract_inverted_index.improvements | 141 |
| abstract_inverted_index.populations. | 150 |
| abstract_inverted_index.expectations, | 36 |
| abstract_inverted_index.meta-analysis | 143 |
| abstract_inverted_index.nomenclature, | 135 |
| abstract_inverted_index.significance. | 50 |
| abstract_inverted_index.Hardy-Weinberg | 34 |
| abstract_inverted_index.disequilibrium | 121 |
| abstract_inverted_index.immunogenetics | 129 |
| abstract_inverted_index.implementation | 116 |
| abstract_inverted_index.infrastructure | 101 |
| abstract_inverted_index.Ewens-Watterson | 38 |
| abstract_inverted_index.colon-delimited | 137 |
| abstract_inverted_index.disequilibrium, | 47 |
| abstract_inverted_index.industry-standard | 109 |
| abstract_inverted_index.https://zenodo.org/records/10080668 | 154 |
| abstract_inverted_index.https://github.com/alexlancaster/pypop | 156 |
| cited_by_percentile_year.max | 98 |
| cited_by_percentile_year.min | 94 |
| corresponding_author_ids | https://openalex.org/A5041658734, https://openalex.org/A5024849718, https://openalex.org/A5003582043 |
| countries_distinct_count | 1 |
| institutions_distinct_count | 6 |
| corresponding_institution_ids | https://openalex.org/I111236770, https://openalex.org/I180670191, https://openalex.org/I4210147267 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/9 |
| sustainable_development_goals[0].score | 0.5899999737739563 |
| sustainable_development_goals[0].display_name | Industry, innovation and infrastructure |
| citation_normalized_percentile.value | 0.8515492 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | True |