Alternatives and similar repositories for scanpy-scripts

Users that are interested in scanpy-scripts are comparing it to the libraries listed below

• czbiohub-sf / tabula-sapiens
  Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens
  ☆42Updated 3 weeks ago
• vib-singlecell-nf / vsn-pipelines
  A repository of pipelines for single-cell data in Nextflow DSL2
  ☆75Updated 2 years ago
• minoda-lab / universc
  UniverSC: a flexible cross-platform single-cell data processing pipeline
  ☆46Updated last year
• cole-trapnell-lab / cicero-release
  ☆59Updated last year
• Novartis / scar
  scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics
  ☆54Updated last year
• KenLauLab / dropkick
  Automated cell filtering for single-cell RNA sequencing data
  ☆25Updated last year
• lcmmichielsen / scHPL
  ☆35Updated 6 months ago
• PoolLab / generecovery
  ☆29Updated 2 years ago
• brianhie / geosketch
  Geometry-preserving random sampling
  ☆89Updated 10 months ago
• dpeerlab / Harmony
  Harmony framework for connecting scRNA-seq data from discrete time points
  ☆50Updated last year
• CFeregrino / scWGCNA
  scWGCNA
  ☆61Updated 2 years ago
• statgen / popscle
  A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and au…
  ☆57Updated 4 years ago
• lanagarmire / SSrGE
  ☆34Updated 6 years ago
• flatironinstitute / inferelator
  Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.
  ☆53Updated last year
• UPSUTER / GEMLI
  ☆32Updated 7 months ago
• Hoohm / CITE-seq-Count
  A tool that allows to get UMI counts from a single cell protein assay
  ☆82Updated 4 months ago
• jmbreda / Sanity
  Filtering of Poison noise on a single-cell RNA-seq UMI count matrix
  ☆78Updated 4 months ago
• alexisvdb / singleCellHaystack
  Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
  ☆85Updated last year
• wenweixiong / MARVEL
  ☆51Updated last year
• DeplanckeLab / ChromatinHD
  High-definition modeling of chromatin + transcriptomics data
  ☆25Updated 5 months ago
• gillislab / MetaNeighbor
  A method to rapidly assess cell type identity using both functional and random gene sets
  ☆39Updated 8 months ago
• vanheeringen-lab / scepia
  Single Cell Epigenome-based Inference of Activity
  ☆19Updated last year
• wbaopaul / scATAC-pro
  A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
  ☆77Updated 6 months ago
• HYsxe / PRINT
  ☆36Updated last year
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆87Updated 3 months ago
• dan-landau / IronThrone-GoT
  processes GoT amplicon data and generates a table of metrics
  ☆32Updated 3 years ago
• morris-lab / Capybara
  Capybara: A computational tool to measure cell identity and fate transitions
  ☆59Updated 3 years ago
• cistrome / MIRA
  Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
  ☆64Updated 2 months ago
• rajewsky-lab / spacemake
  ☆44Updated last month
• fmicompbio / adv_singlecell_2022
  Material for the "Advanced topics in single-cell analysis" course (2022 edition)
  ☆17Updated 3 years ago