Alternatives and similar repositories for SUPPA

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

• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆267Updated last week
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆243Updated last week
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆213Updated this week
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆217Updated last week
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆327Updated 4 years ago
• Xinglab / rmats-turbo
  ☆279Updated 3 weeks ago
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆299Updated 2 years ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆251Updated last month
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆260Updated 2 years ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆226Updated 4 months ago
• jsh58 / Genrich
  Detecting sites of genomic enrichment
  ☆196Updated 2 years ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆274Updated 2 years ago
• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆256Updated 3 months ago
• ablab / IsoQuant
  Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
  ☆192Updated last week
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆139Updated 5 years ago
• ENCODE-DCC / rna-seq-pipeline
  ☆157Updated 3 years ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆250Updated 4 months ago
• BrooksLabUCSC / flair
  Full-Length Alternative Isoform analysis of RNA
  ☆239Updated last week
• VanLoo-lab / ascat
  ASCAT R package
  ☆190Updated last month
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆180Updated last week
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆154Updated last year
• davidaknowles / leafcutter
  Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae …
  ☆226Updated last year
• loosolab / TOBIAS
  Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
  ☆230Updated 2 months ago
• nf-core / chipseq
  ChIP-seq peak-calling, QC and differential analysis pipeline.
  ☆226Updated 3 weeks ago
• haowenz / chromap
  Fast alignment and preprocessing of chromatin profiles
  ☆206Updated last month
• Xinglab / rmats2sashimiplot
  ☆153Updated 5 months ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆346Updated 2 months ago
• sdparekh / zUMIs
  zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
  ☆286Updated last year
• broadinstitute / ichorCNA
  Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
  ☆191Updated last year
• nloyfer / wgbs_tools
  tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
  ☆171Updated 5 months ago