sdjebali
Initially trained as a computer scientist, I did my phD on gene finding (Exogean), and then participated to many functional annotation consortia (ENCODE, FAANG)
INSERMToulouse, France
Pinned Repositories
ChimPipe
ChimPipe: Accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data
Exogean
A program for eukaryotic gene identification based on heuristic rules used by human experts
grape-nf
An automated RNA-seq pipeline using Nextflow
atac_pipe
Simple pipeline for processing paired end ATAC-seq data
Comptr
Compare two sets of transcripts in terms of intron chain
EnhancerGene
This is a repository for scripts and programs developped for the identification of enhancer/gene relationships in animal genomes
MakeGencodeTSS
Makes distinct TSS of each gene from a Gencode annotation
MakeSP
Compute segmented projections from an annotation
Overlap
Intersect two sets of genomic segments in gff2 format
Scripts
Bash, awk, R, python scripts and binaries for genomic and transcriptomic data analysis
sdjebali's Repositories
sdjebali/MakeGencodeTSS
Makes distinct TSS of each gene from a Gencode annotation
sdjebali/Scripts
Bash, awk, R, python scripts and binaries for genomic and transcriptomic data analysis
sdjebali/Comptr
Compare two sets of transcripts in terms of intron chain
sdjebali/EnhancerGene
This is a repository for scripts and programs developped for the identification of enhancer/gene relationships in animal genomes
sdjebali/Overlap
Intersect two sets of genomic segments in gff2 format
sdjebali/atac_pipe
Simple pipeline for processing paired end ATAC-seq data
sdjebali/MakeSP
Compute segmented projections from an annotation
sdjebali/Compmerge
Merges transcripts with compatible intron chains
sdjebali/docs
Documentation for SeqOccin SV project
sdjebali/DuplSeq
Computes direct repeats at junction boundaries (including chimeric junctions)
sdjebali/FilterSmallPseudo
Filters out small transcripts and pseudogenes from a Gencode annotation file in gtf format
sdjebali/fragencode-atacseq-pipeline
This is the pipeline to process ATAC-seq data from fastq to peaks used in the FR-AgENCODE project
sdjebali/fragencode-rnaseq-mapquantassemble
This is the pipeline to process RNA-seq data from fastq to reference and new transcript and gene expression used in the FR-AgENCODE project
sdjebali/MakeGencCAGETSS
Makes TSS clusters from Gencode TSS and CAGE peaks
sdjebali/PaintorPipe
Pipeline to run the Paintor program and its associated visualization tools on GWAS summary statistics data
sdjebali/sdjebali.github.io
Sarah Djebali's personal website.
sdjebali/smrnaseq
A small-RNA sequencing analysis pipeline