wdecoster / DEA.RLinks
Script to automate differential expression analysis using DESeq2, edgeR or limma-voom
☆20Updated 7 years ago
Alternatives and similar repositories for DEA.R
Users that are interested in DEA.R are comparing it to the libraries listed below
Sorting:
- RNA-Sequencing data differential expression analysis pipeline. Performs: genome coverage (via bedtools and HTSeq), generates Circos code …☆56Updated 13 years ago
- Rna-seq pipeline, From FASTQ to differential expression analysis...☆20Updated 8 years ago
- A toolkit for QC and visualization of ATAC-seq results.☆73Updated last year
- ATAC-seq Quality Control☆25Updated 3 months ago
- ATAC-seq lab for BIOINF545☆24Updated 11 months ago
- A collection of resources to filter 'bad' probes from the Illumina 450k and EPIC methylation arrays☆29Updated 2 years ago
- deepStats: a stastitical toolbox for deeptools and genomic signals☆35Updated 4 years ago
- Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data☆67Updated 5 years ago
- RNAseq pipeline based on snakemake☆26Updated 2 years ago
- ☆75Updated 2 years ago
- RNA-seq workflow: differential transcript usage☆23Updated 2 years ago
- HMMRATAC peak caller for ATAC-seq data☆98Updated last year
- R package for bcbio RNA-seq analysis.☆63Updated last year
- A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.☆37Updated 4 years ago
- A preprocessing and QC pipeline for HiChIP data☆40Updated 3 years ago
- This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to…☆62Updated 5 years ago
- Genomic Association Tester☆35Updated 2 years ago
- RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.☆41Updated 3 years ago
- Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19☆77Updated 3 weeks ago
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆100Updated 4 years ago
- An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.☆72Updated last year
- Exome/Capture/RNASeq Pipeline Implementation using snakemake☆47Updated 7 years ago
- Pipeline for finding circular RNAs from RNA-seq data, based on STAR. Used in (Westholm et al, Cell Reports, 2014).☆17Updated 3 years ago
- A toolkit for working with ATAC-seq data.☆24Updated 2 weeks ago
- Portable eQTL analysis and statistical fine mapping workflow used by the eQTL Catalogue☆57Updated 4 months ago
- Unsorted scripts for bioinformatics☆61Updated 4 years ago
- An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)☆124Updated this week
- ☆14Updated 9 years ago
- Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.☆51Updated 7 years ago
- Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each alle…☆44Updated 3 years ago