Baraa Orabi
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View article: TKSM: highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator
TKSM: highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator Open
Motivation Transcriptomic long-read (LR) sequencing is an increasingly cost-effective technology for probing various RNA features. Numerous tools have been developed to tackle various transcriptomic sequencing tasks (e.g. isoform and gene …
View article: TKSM: Highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator
TKSM: Highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator Open
Motivation Transcriptomic long-read (LR) sequencing is an increasingly cost-effective technology for probing various RNA features. Numerous tools have been developed to tackle various transcriptomic sequencing tasks (e.g. isoform and gene …
View article: Small chr21 dataset
Small chr21 dataset Open
Small TKSM dataset with refs.Reads are subsampled from MCF7 cell line (direct RNA, replicate 1, run 2) of https://registry.opendata.aws/sgnex/
View article: Small test data for TKSM
Small test data for TKSM Open
Small test data for TKSM simulator (https://github.com/vpc-ccg/tksm)
View article: N1 single-cell barcoded RNA-seq ONT long-reads
N1 single-cell barcoded RNA-seq ONT long-reads Open
The dataset is extracted from an RNA human sample. The RNA molecules have 10x Genomics single-cell barcodes + UMI + Illumina read adapters added to them. Then the ONT long-read adatper is added. The library structure is explained in our pr…
View article: Freddie: annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing
Freddie: annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing Open
Alternative splicing (AS) is an important mechanism in the development of many cancers, as novel or aberrant AS patterns play an important role as an independent onco-driver. In addition, cancer-specific AS is potentially an effective targ…
View article: Fast and accurate matching of cellular barcodes across short-reads and long-reads of single-cell RNA-seq experiments
Fast and accurate matching of cellular barcodes across short-reads and long-reads of single-cell RNA-seq experiments Open
Single-cell RNA sequencing allows for characterizing the gene expression landscape at the cell type level. However, because of its use of short-reads, it is severely limited at detecting full-length features of transcripts such as alternat…
View article: scTagger: Fast and accurate matching of cellular barcodes across short- and long-reads of single-cell RNA-seq experiments
scTagger: Fast and accurate matching of cellular barcodes across short- and long-reads of single-cell RNA-seq experiments Open
Summary Single-cell RNA sequencing allows for characterizing the gene expression landscape at the cell type level. However, because of its use of short-reads, it is severely limited at detecting full-length features of transcripts such as …
View article: Simulation data
Simulation data Open
Simulation dataset used in the paper. The short and long-reads are present. The long-reads have been converted to FASTA format to save on space.
View article: Trimmed real datasets
Trimmed real datasets Open
Long-reads of the real datasets. The reads are trimmed to removed any human RNA sequences and to keep the interval of the read that includes the Illumani adapter and the 10x barcdoes. Top short-read barcodes. The selected barcodes of the …
View article: Freddie: Annotation-independent Detection and Discovery of Transcriptomic Alternative Splicing Isoforms
Freddie: Annotation-independent Detection and Discovery of Transcriptomic Alternative Splicing Isoforms Open
Alternative splicing (AS) is an important mechanism in the development of many cancers, as novel or aberrant AS patterns play an important role as an independent onco-driver. In addition, cancer-specific AS is potentially an effective targ…
View article: Structural variation and fusion detection using targeted sequencing data from circulating cell free DNA
Structural variation and fusion detection using targeted sequencing data from circulating cell free DNA Open
SViCT is available at https://github.com/vpc-ccg/svict. Contact:[email protected].
View article: Alignment-free clustering and error correction of UMI tagged DNA molecules
Alignment-free clustering and error correction of UMI tagged DNA molecules Open
The use of circulating tumour DNA (ctDNA) in cancer oncogenomics has the potential for rapid and non-invasive monitoring of patient-specific tumour progression. However, detection of low allele frequency variations in ctDNA raises many cha…