Alternatives and similar repositories for pydeseq2

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

• s-andrews / sradownloader
  A script to make downloading of SRA/GEO data easier
  ☆31Updated last year
• fulcrumgenomics / python-snakemake-template
  A template repository for Snakemake pipepline(s) and a python command-line toolkit.
  ☆28Updated last month
• TRON-Bioinformatics / tronflow-hla-hd
  A Nextflow workflow for HLA typing using HLA-HD
  ☆11Updated 11 months ago
• derijkp / scywalker
  A program for the analysis of single cell nanopore long read data
  ☆19Updated last week
• ulelab / ultraplex
  Ultra-fast 5' and 3' demultiplexer
  ☆27Updated last year
• XueyiDong / LongReadBenchmark
  Benchmarking long-read RNA-seq analysis tools
  ☆27Updated 4 months ago
• gagneurlab / absplice
  ☆39Updated 9 months 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
• 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
• crazyhottommy / pyflow-RNAseq
  RNAseq pipeline based on snakemake
  ☆26Updated 2 years ago
• cortes-ciriano-lab / ReConPlot
  ☆22Updated 6 months ago
• bjmt / universalmotif
  Motif manipulation functions for R.
  ☆29Updated 2 months ago
• complextissue / pytximport
  Feature-rich Python implementation of the tximport package for gene count estimation.
  ☆36Updated last month
• mortazavilab / swan_vis
  A Python library to visualize and analyze long-read transcriptomes
  ☆62Updated last month
• zhongw2 / GeneTEFlow
  ☆23Updated 4 years ago
• hoffmangroup / umap
  ☆26Updated 2 months ago
• broadinstitute / longbow
  Annotation and segmentation of MAS-seq data
  ☆20Updated 2 years ago
• tgen / bisbee
  alternative splicing analysis pipeline
  ☆19Updated 4 years ago
• splicebox / MntJULiP
  Comprehensive and scalable differential splicing analyses
  ☆17Updated 3 months ago
• mehdiborji / nanoranger
  simplified cellranger for long-read data
  ☆19Updated 2 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
• nf-core / circdna
  Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from…
  ☆31Updated 3 weeks ago
• jfjlaros / demultiplex
  Versatile FASTA/FASTQ demultiplexer.
  ☆33Updated last year
• mritchielab / GlimmaV2
  interactive plots for differential expression analysis
  ☆32Updated last week
• YangLab / CLEAR
  direct comparison of circular and linear RNA expression
  ☆23Updated 4 years ago
• nf-core / rnasplice
  rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis
  ☆54Updated 3 weeks ago
• Xinglab / CLAM
  CLIP-seq Analysis of Multi-mapped reads
  ☆30Updated 3 years ago
• WGLab / LIQA
  Long-read Isoform Quantification and Analysis
  ☆38Updated 3 months ago
• jsh58 / DMRfinder
  Identifying differentially methylated regions from MethylC-seq (bisulfite-sequencing) data
  ☆28Updated 2 years ago
• songlab-cal / scquint
  ☆17Updated last year