Alternatives and similar repositories for pydeseq2

Users that are interested in pydeseq2 are comparing it to the libraries listed below

• complextissue / pytximport
  Feature-rich Python implementation of the tximport package for gene count estimation.
  ☆36Updated last week
• derijkp / scywalker
  A program for the analysis of single cell nanopore long read data
  ☆19Updated 2 months ago
• fulcrumgenomics / python-snakemake-template
  A template repository for Snakemake pipepline(s) and a python command-line toolkit.
  ☆28Updated last month
• hsinyenwu / RiboPlotR
  RiboPlotR package for Ribo-plot
  ☆15Updated last year
• s-andrews / sradownloader
  A script to make downloading of SRA/GEO data easier
  ☆30Updated last year
• hoffmangroup / umap
  ☆26Updated 2 months ago
• jfjlaros / demultiplex
  Versatile FASTA/FASTQ demultiplexer.
  ☆33Updated last year
• mehdiborji / nanoranger
  simplified cellranger for long-read data
  ☆19Updated last month
• XueyiDong / LongReadBenchmark
  Benchmarking long-read RNA-seq analysis tools
  ☆27Updated 3 months ago
• crazyhottommy / pyflow-RNAseq
  RNAseq pipeline based on snakemake
  ☆26Updated 2 years ago
• gagneurlab / absplice
  ☆39Updated 8 months ago
• bernardo-de-almeida / motif-clustering
  Clustering TF motif models from multiple species (mostly focused on Drosophila and human) by similarity to remove redundancy
  ☆26Updated 2 years ago
• TrinityCTAT / CTAT-VirusIntegrationFinder
  ☆16Updated last year
• Kingsford-Group / squid
  SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
  ☆42Updated 3 years ago
• comprna / MoSEA
  Motif Scan and Enrichment Analysis (MoSEA)
  ☆16Updated 4 years ago
• splicebox / MntJULiP
  Comprehensive and scalable differential splicing analyses
  ☆17Updated 2 months ago
• mortazavilab / swan_vis
  A Python library to visualize and analyze long-read transcriptomes
  ☆62Updated last month
• broadinstitute / longbow
  Annotation and segmentation of MAS-seq data
  ☆20Updated 2 years ago
• bjmt / universalmotif
  Motif manipulation functions for R.
  ☆28Updated last month
• huishenlab / biscuit
  BISulfite-seq CUI Toolkit
  ☆19Updated 3 weeks ago
• Dowell-Lab / TFEA
  Transcription Factor Enrichment Analysis
  ☆34Updated last month
• nf-core / rnasplice
  rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis
  ☆54Updated last month
• cortes-ciriano-lab / ReConPlot
  ☆22Updated 5 months ago
• mritchielab / GlimmaV2
  interactive plots for differential expression analysis
  ☆32Updated 2 months ago
• ben-laufer / CpG_Me
  A whole genome bisulfite sequencing (WGBS) pipeline for the alignment and QC of DNA methylation that goes from from raw reads (FastQ) to …
  ☆23Updated 3 years ago
• zhongw2 / GeneTEFlow
  ☆23Updated 4 years ago
• seqcode / allo
  Allo: a multi-mapped read rescue strategy for gene regulatory analyses
  ☆24Updated 9 months ago
• kundajelab / idr
  IDR
  ☆31Updated 2 years ago
• pachterlab / sircel
  Identify cell barcodes from single-cell genomics sequencing experiments
  ☆43Updated 3 years ago
• JSB-UCLA / Clipper
  A p-value-free method for controlling false discovery rates in high-throughput biological data with two conditions
  ☆39Updated 2 years ago