Alternatives and similar repositories for SQANTI3

Users that are interested in SQANTI3 are comparing it to the libraries listed below

• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆219Updated last month
• GoekeLab / bambu
  Reference-guided transcript discovery and quantification for long read RNA-Seq data
  ☆216Updated last week
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆258Updated 6 months ago
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆279Updated last year
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆273Updated last year
• ablab / IsoQuant
  Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
  ☆176Updated last week
• BrooksLabUCSC / flair
  Full-Length Alternative Isoform analysis of RNA
  ☆233Updated this week
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆239Updated last month
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆245Updated this week
• rpetit3 / fastq-dl
  Download FASTQ files from SRA or ENA repositories.
  ☆340Updated 2 months ago
• haowenz / chromap
  Fast alignment and preprocessing of chromatin profiles
  ☆203Updated 3 weeks ago
• ENCODE-DCC / rna-seq-pipeline
  ☆154Updated 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 last month
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆153Updated last year
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆170Updated 2 weeks ago
• Xinglab / rmats-turbo
  ☆270Updated 9 months ago
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆108Updated 2 years ago
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆216Updated last month
• mortazavilab / TALON
  Technology agnostic long read analysis pipeline for transcriptomes
  ☆149Updated last year
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆208Updated last month
• GoekeLab / sg-nex-data
  Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
  ☆134Updated this week
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆299Updated 2 years ago
• im3sanger / dndscv
  dN/dS methods to quantify selection in cancer and somatic evolution
  ☆223Updated 3 months ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆273Updated 6 months ago
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆125Updated 2 years ago
• jsh58 / Genrich
  Detecting sites of genomic enrichment
  ☆192Updated 2 years ago
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆192Updated this week
• Xinglab / rmats2sashimiplot
  ☆149Updated 3 months ago
• CompEpigen / figeno
  Tool for plotting sequencing data along genomic coordinates.
  ☆308Updated last month
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆257Updated 2 years ago