Alternatives and similar repositories for sleuth

Users that are interested in sleuth are comparing it to the libraries listed below

• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆267Updated 2 years ago
• PoisonAlien / maftools
  Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
  ☆467Updated last week
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆342Updated 11 months ago
• thelovelab / DESeq2
  Differential expression of RNA-seq data using the Negative Binomial
  ☆401Updated last month
• bernatgel / karyoploteR
  karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
  ☆324Updated last month
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆444Updated last year
• broadinstitute / gtex-pipeline
  GTEx & TOPMed data production and analysis pipelines
  ☆374Updated last month
• YuLab-SMU / ChIPseeker
  ChIP peak Annotation, Comparison and Visualization
  ☆237Updated 2 months ago
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆389Updated 7 months ago
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆399Updated 2 weeks ago
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆313Updated 4 years ago
• sdparekh / zUMIs
  zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
  ☆281Updated last year
• al2na / methylKit
  R package for DNA methylation analysis
  ☆232Updated 4 months ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆425Updated 2 months ago
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆242Updated 2 years ago
• CGATOxford / UMI-tools
  Tools for handling Unique Molecular Identifiers in NGS data sets
  ☆515Updated this week
• hbctraining / DGE_workshop
  ☆394Updated 3 years ago
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆298Updated 2 years ago
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆343Updated 2 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 …
  ☆221Updated last year
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆214Updated 3 months ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆254Updated 2 years ago
• pachterlab / kallisto
  Near-optimal RNA-Seq quantification
  ☆693Updated 3 months ago
• crazyhottommy / bioinformatics-one-liners
  Bioinformatics one liners from Ming Tang
  ☆487Updated 4 years ago
• hbctraining / Intro-to-DGE
  ☆202Updated 3 months ago
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆422Updated 6 months ago
• hbctraining / Intro-to-rnaseq-hpc-O2
  This repository has teaching materials for a 2 and 3-day Introduction to RNA-sequencing data analysis workshop using the O2 Cluster
  ☆170Updated 4 years ago
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆335Updated 3 weeks ago
• hbctraining / Intro-to-ChIPseq
  Intro to ChIPseq using HPC
  ☆309Updated 2 years ago
• alserglab / fgsea
  Fast Gene Set Enrichment Analysis
  ☆409Updated last week