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
  ☆266Updated 2 years ago
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆454Updated last year
• PoisonAlien / maftools
  Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
  ☆478Updated 3 months ago
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆299Updated 2 years ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆346Updated last month
• bernatgel / karyoploteR
  karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
  ☆345Updated 4 months ago
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆401Updated 2 months ago
• broadinstitute / gtex-pipeline
  GTEx & TOPMed data production and analysis pipelines
  ☆384Updated last month
• al2na / methylKit
  R package for DNA methylation analysis
  ☆238Updated last month
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆324Updated 4 years ago
• YuLab-SMU / ChIPseeker
  ChIP peak Annotation, Comparison and Visualization
  ☆239Updated last week
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆243Updated 2 years ago
• thelovelab / DESeq2
  Differential expression of RNA-seq data using the Negative Binomial
  ☆418Updated last week
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆434Updated 2 months ago
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆397Updated this week
• davidaknowles / leafcutter
  Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae …
  ☆225Updated last year
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆219Updated 3 weeks ago
• CGATOxford / UMI-tools
  Tools for handling Unique Molecular Identifiers in NGS data sets
  ☆526Updated 3 months ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆260Updated 2 years ago
• hbctraining / DGE_workshop
  ☆401Updated 3 years ago
• ewels / sra-explorer
  Web application to explore the Sequence Read Archive.
  ☆217Updated 3 months ago
• sdparekh / zUMIs
  zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
  ☆286Updated last year
• hbctraining / Intro-to-DGE
  ☆209Updated 2 months ago
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆352Updated 5 months ago
• im3sanger / dndscv
  dN/dS methods to quantify selection in cancer and somatic evolution
  ☆226Updated 5 months ago
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆527Updated last month
• hbctraining / Training-modules
  Materials for short, half-day workshops
  ☆339Updated last month
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆275Updated 2 years ago
• ENCODE-DCC / chip-seq-pipeline2
  ENCODE ChIP-seq pipeline
  ☆274Updated last year
• hbctraining / In-depth-NGS-Data-Analysis-Course
  ☆442Updated 5 years ago