ConesaLab / SQANTI3

Related projects ⓘ

Alternatives and complementary repositories for SQANTI3

• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆192Updated 3 weeks ago
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆228Updated 3 weeks ago
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆128Updated last year
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆205Updated 4 months ago
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆106Updated last year
• ablab / IsoQuant
  Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
  ☆153Updated this week
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆253Updated 4 months ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆257Updated last year
• GoekeLab / bambu
  Reference-guided transcript discovery and quantification for long read RNA-Seq data
  ☆189Updated last week
• BrooksLabUCSC / flair
  Full-Length Alternative Isoform analysis of RNA
  ☆213Updated last week
• rpetit3 / fastq-dl
  Download FASTQ files from SRA or ENA repositories.
  ☆276Updated last month
• haowenz / chromap
  Fast alignment and preprocessing of chromatin profiles
  ☆192Updated last week
• VanLoo-lab / ascat
  ASCAT R package
  ☆168Updated 3 weeks ago
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆188Updated last month
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆262Updated 5 months ago
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆140Updated 2 months ago
• jsh58 / Genrich
  Detecting sites of genomic enrichment
  ☆187Updated last year
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆104Updated last year
• GoekeLab / sg-nex-data
  Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
  ☆111Updated last month
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆231Updated 2 weeks ago
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆125Updated 2 years ago
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆283Updated 3 weeks ago
• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆233Updated last month
• signalbash / how_are_we_stranded_here
  Check strandedness of RNA-Seq fastq files
  ☆115Updated 2 years ago
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆140Updated this week
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆243Updated last year
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆200Updated 2 weeks ago
• nf-core / nanoseq
  Nanopore demultiplexing, QC and alignment pipeline
  ☆179Updated last week
• nf-core / fetchngs
  Pipeline to fetch metadata and raw FastQ files from public databases
  ☆152Updated last week
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆226Updated 2 weeks ago