macarthur-lab / gene_lists

Related projects ⓘ

Alternatives and complementary repositories for gene_lists

• broadinstitute / gtex-pipeline
  GTEx & TOPMed data production and analysis pipelines
  ☆342Updated 7 months ago
• davidaknowles / leafcutter
  Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae …
  ☆208Updated 5 months ago
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆200Updated 2 weeks ago
• kundajelab / atac_dnase_pipelines
  ATAC-seq and DNase-seq processing pipeline
  ☆162Updated 2 years ago
• daler / pybedtools
  Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
  ☆310Updated 2 weeks ago
• pachterlab / sleuth
  Differential analysis of RNA-Seq
  ☆305Updated 4 months ago
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆273Updated 3 years ago
• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆259Updated last year
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆375Updated 4 months ago
• simon-anders / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆122Updated 4 years ago
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆234Updated last year
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆243Updated last year
• konradjk / loftee
  ☆174Updated last year
• ENCODE-DCC / chip-seq-pipeline
  ENCODE Uniform processing pipeline for ChIP-seq
  ☆120Updated 4 years ago
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆134Updated 4 years ago
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆312Updated 3 weeks ago
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆366Updated 11 months ago
• im3sanger / dndscv
  dN/dS methods to quantify selection in cancer and somatic evolution
  ☆212Updated last year
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆305Updated 2 years ago
• Hoohm / dropSeqPipe
  A SingleCell RNASeq pre-processing snakemake workflow
  ☆147Updated last year
• macarthur-lab / clinvar
  This repo provides tools to convert ClinVar data into a tab-delimited flat file, and also provides that resulting tab-delimited flat file…
  ☆122Updated 4 years ago
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆283Updated last year
• deeptools / pyBigWig
  A python extension for quick access to bigWig and bigBed files
  ☆218Updated 3 months ago
• FRED-2 / OptiType
  Precision HLA typing from next-generation sequencing data
  ☆190Updated 8 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆530Updated 4 months ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆257Updated last year
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆188Updated last month
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆226Updated 2 weeks ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆327Updated 3 months ago
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆228Updated 3 weeks ago