Alternatives and similar repositories for pycistarget

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

• HYsxe / PRINT
  ☆37Updated last year
• timoast / sinto
  Tools for single-cell data processing
  ☆132Updated last year
• CostaLab / reg-gen
  Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
  ☆111Updated 3 months ago
• vib-singlecell-nf / vsn-pipelines
  A repository of pipelines for single-cell data in Nextflow DSL2
  ☆80Updated 2 years ago
• nf-core / spatialvi
  Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcri…
  ☆71Updated this week
• aertslab / pycisTopic
  pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
  ☆79Updated last week
• chung-lab / SCAFE
  Single Cell Analysis of Five'Ends
  ☆50Updated last year
• 10XGenomics / subset-bam
  ☆82Updated 2 years ago
• JonathanShor / DoubletDetection
  Doublet detection in single-cell RNA-seq data.
  ☆97Updated last year
• single-cell-genetics / cellsnp-lite
  Efficient genotyping bi-allelic SNPs on single cells
  ☆157Updated 3 months ago
• aertslab / create_cisTarget_databases
  Create cisTarget databases
  ☆55Updated 7 months ago
• deweylab / CellO
  CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology
  ☆68Updated 2 years ago
• KChen-lab / Monopogen
  SNV calling from single cell sequencing
  ☆120Updated last year
• UcarLab / AMULET
  A count based method for detecting doublets from single nucleus ATAC-seq (snATAC-seq) data.
  ☆32Updated 3 years ago
• chris-mcginnis-ucsf / MULTI-seq
  R implementation of MULTI-seq sample classification workflow
  ☆66Updated 2 years ago
• pinellolab / dictys
  Context specific and dynamic gene regulatory network reconstruction and analysis
  ☆127Updated 2 months ago
• caleblareau / mgatk
  mgatk: mitochondrial genome analysis toolkit
  ☆110Updated last year
• tanlongzhi / dip-c
  Tools to analyze Dip-C (or other 3C/Hi-C) data
  ☆74Updated last year
• Hoohm / CITE-seq-Count
  A tool that allows to get UMI counts from a single cell protein assay
  ☆87Updated 9 months ago
• bioinfo-ibms-pumc / SCSA
  SCSA: cell type annotation for single-cell RNA-seq data
  ☆94Updated 2 years ago
• theislab / anndata2ri
  Convert between AnnData and SingleCellExperiment
  ☆143Updated last week
• statgen / popscle
  A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and au…
  ☆58Updated 4 years ago
• pachterlab / kallistobustools
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data
  ☆119Updated 3 years ago
• AllonMKlein / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆86Updated 6 years ago
• parashardhapola / scarf
  Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with mill…
  ☆112Updated 2 months ago
• atarashansky / SAMap
  SAMap: Mapping single-cell RNA sequencing datasets from evolutionarily distant organisms.
  ☆88Updated last month
• lhqing / ALLCools
  Toolkit for single-cell DNA methylation analysis.
  ☆46Updated 3 weeks ago
• single-cell-genetics / cellSNP
  Pileup biallelic SNPs from single-cell and bulk RNA-seq data
  ☆83Updated 3 years ago
• kharchenkolab / dropEst
  Pipeline for initial analysis of droplet-based single-cell RNA-seq data
  ☆95Updated 3 years ago
• jmbreda / Sanity
  Filtering of Poison noise on a single-cell RNA-seq UMI count matrix
  ☆79Updated 2 months ago