Alternatives and similar repositories for ballgown:

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

• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆211Updated 7 months ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆156Updated last year
• OpenGene / AfterQC
  Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
  ☆209Updated 4 years ago
• Zhong-Lab-UCSD / Genomic-Interactive-Visualization-Engine
  Genomic Interactive Visualization Engine
  ☆145Updated 2 years ago
• shenwei356 / bio_scripts
  Practical, reusable scripts for bioinformatics
  ☆98Updated 6 years ago
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆130Updated 9 years ago
• Czh3 / NGSTools
  Next-Generation Sequencing(NGS) toolkits.
  ☆45Updated 8 years ago
• alimanfoo / pysamstats
  A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM …
  ☆194Updated 2 weeks ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆192Updated last year
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆136Updated 4 years ago
• NAL-i5K / GFF3toolkit
  Python programs for processing GFF3 files
  ☆96Updated 10 months ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆202Updated 3 months ago
• GoekeLab / sg-nex-data
  Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
  ☆115Updated last month
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆142Updated 5 months ago
• maasha / biopieces
  Biopieces is a bioinformatic framework of tools easily used and easily created.
  ☆141Updated 6 years ago
• zhxiaokang / RASflow
  RNA-Seq analysis workflow
  ☆104Updated 3 years ago
• genome / breakdancer
  SV detection from paired end reads mapping
  ☆117Updated 5 years ago
• ExpressionAnalysis / ea-utils
  Automatically exported from code.google.com/p/ea-utils
  ☆95Updated last year
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆157Updated 5 months ago
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆240Updated last week
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆144Updated last year
• lima1 / PureCN
  Copy number calling and variant classification using targeted short read sequencing
  ☆132Updated 3 weeks ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆111Updated 7 months ago
• ENCODE-DCC / chip-seq-pipeline
  ENCODE Uniform processing pipeline for ChIP-seq
  ☆122Updated 4 years ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆312Updated 3 years ago
• mdshw5 / fastqp
  Simple FASTQ quality assessment using Python
  ☆109Updated 3 years ago
• biostars / biostar-handbook
  Issue tracker for the Biostar Handbook
  ☆61Updated 2 years ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 3 months ago
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆194Updated 3 years ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆261Updated last year