sdjebali

Sarah Djebali's repositories

MakeGencodeTSS

Makes distinct TSS of each gene from a Gencode annotation

Language:Shell10 30

Scripts

Bash, awk, R, python scripts and binaries for genomic and transcriptomic data analysis

Language:ShellGPL-2.09 30

Comptr

Compare two sets of transcripts in terms of intron chain

Language:OCaml1 2 1

EnhancerGene

This is a repository for scripts and programs developped for the identification of enhancer/gene relationships in animal genomes

Language:PythonGPL-3.01 20

Overlap

Intersect two sets of genomic segments in gff2 format

Language:OCamlApache-2.01 20

atac_pipe

Simple pipeline for processing paired end ATAC-seq data

Language:Shell020

MakeSP

Compute segmented projections from an annotation

Language:OCamlApache-2.0020

Compmerge

Merges transcripts with compatible intron chains

Language:OCaml020

docs

Documentation for SeqOccin SV project

020

DuplSeq

Computes direct repeats at junction boundaries (including chimeric junctions)

Language:OCamlApache-2.0020

FilterSmallPseudo

Filters out small transcripts and pseudogenes from a Gencode annotation file in gtf format

Language:Shell020

fragencode-atacseq-pipeline

This is the pipeline to process ATAC-seq data from fastq to peaks used in the FR-AgENCODE project

Language:Python020

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

Language:Python000

MakeGencCAGETSS

Makes TSS clusters from Gencode TSS and CAGE peaks

Language:Shell020

PaintorPipe

Pipeline to run the Paintor program and its associated visualization tools on GWAS summary statistics data

Language:HTMLGPL-3.002 2

smrnaseq

A small-RNA sequencing analysis pipeline

Language:NextflowMIT010