Alternatives and similar repositories for intervene:

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

• ncbi / TPMCalculator
  TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files
  ☆128Updated 8 months ago
• guigolab / ggsashimi
  Command-line tool for the visualization of splicing events across multiple samples
  ☆128Updated 7 months ago
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆119Updated 2 years ago
• dpryan79 / MethylDackel
  A (mostly) universal methylation extractor for BS-seq experiments.
  ☆169Updated 8 months ago
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆108Updated 3 weeks ago
• zhxiaokang / RASflow
  RNA-Seq analysis workflow
  ☆104Updated 3 years ago
• vastgroup / vast-tools
  A toolset for profiling alternative splicing events in RNA-Seq data.
  ☆80Updated 3 weeks ago
• harbourlab / SparK
  Publication quality NGS track plotting
  ☆111Updated 2 years ago
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆100Updated 3 months ago
• PoisonAlien / trackplot
  Generate IGV style locus tracks from bigWig files in R
  ☆154Updated 3 months ago
• jsh58 / Genrich
  Detecting sites of genomic enrichment
  ☆190Updated last year
• CRG-Barcelona / bwtool
  A tool for bigWig files.
  ☆119Updated 6 years ago
• sheynkman-lab / Long-Read-Proteogenomics
  A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.
  ☆43Updated 2 years ago
• nf-core / hic
  Analysis of Chromosome Conformation Capture data (Hi-C)
  ☆95Updated 3 weeks ago
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆107Updated 2 years ago
• CRG-CNAG / CalliNGS-NF
  GATK RNA-Seq Variant Calling in Nextflow
  ☆132Updated 2 years ago
• GoekeLab / sg-nex-data
  Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
  ☆116Updated last month
• htseq / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆100Updated 3 months ago
• nf-core / differentialabundance
  Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
  ☆72Updated this week
• TrinityCTAT / Trinity_CTAT
  ☆116Updated last year
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆206Updated this week
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆136Updated 4 years ago
• nf-core / smrnaseq
  A small-RNA sequencing analysis pipeline
  ☆79Updated 3 weeks ago
• ShiLab-Bioinformatics / subread
  The Subread software package is a tool kit for processing next-gen sequencing data. It includes Subread aligner, Subjunc exon-exon juncti…
  ☆41Updated last year
• RabadanLab / arcasHLA
  Fast and accurate in silico inference of HLA genotypes from RNA-seq
  ☆123Updated 6 months ago
• caleblareau / mgatk
  mgatk: mitochondrial genome analysis toolkit
  ☆107Updated last month
• kundajelab / phantompeakqualtools
  This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to…
  ☆56Updated 4 years ago
• csoneson / ARMOR
  Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data
  ☆162Updated 2 months ago
• hzi-bifo / RiboDetector
  Accurate and rapid RiboRNA sequences Detector based on deep learning
  ☆105Updated last year
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆54Updated 2 years ago