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
  ☆204Updated this week
• GoekeLab / bambu
  Reference-guided transcript discovery and quantification for long read RNA-Seq data
  ☆199Updated this week
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆141Updated last year
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆212Updated 7 months ago
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆240Updated last month
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆261Updated last year
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆271Updated 8 months ago
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆107Updated 2 years ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆261Updated 3 weeks ago
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆144Updated 6 months ago
• BrooksLabUCSC / flair
  Full-Length Alternative Isoform analysis of RNA
  ☆219Updated this week
• ablab / IsoQuant
  Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
  ☆157Updated this week
• epi2me-labs / wf-transcriptomes
  ☆88Updated 2 months ago
• GoekeLab / sg-nex-data
  Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
  ☆116Updated last month
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆135Updated 3 years ago
• ewels / sra-explorer
  Web application to explore the Sequence Read Archive.
  ☆210Updated last month
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆205Updated 3 weeks ago
• haowenz / chromap
  Fast alignment and preprocessing of chromatin profiles
  ☆196Updated 3 months ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆244Updated 3 months ago
• rpetit3 / fastq-dl
  Download FASTQ files from SRA or ENA repositories.
  ☆303Updated 4 months ago
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆136Updated 4 years ago
• jsh58 / Genrich
  Detecting sites of genomic enrichment
  ☆190Updated last year
• VanLoo-lab / ascat
  ASCAT R package
  ☆175Updated 2 months ago
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆197Updated last week
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆119Updated 2 years ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆247Updated last year
• kcleal / gw
  Genome browser and variant annotation
  ☆295Updated last week
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆298Updated 2 weeks ago
• Xinglab / rmats-turbo
  ☆241Updated 3 months ago
• ENCODE-DCC / rna-seq-pipeline
  ☆146Updated 2 years ago