Alternatives and similar repositories for single-cell-best-practices

Users that are interested in single-cell-best-practices are comparing it to the libraries listed below

• mdozmorov / scRNA-seq_notes
  A list of scRNA-seq analysis tools
  ☆712Updated last week
• theislab / single-cell-tutorial
  Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq an…
  ☆1,498Updated 2 years ago
• hbctraining / Intro-to-scRNAseq
  ☆607Updated 3 months ago
• Starlitnightly / omicverse
  A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
  ☆677Updated this week
• hbctraining / scRNA-seq
  ☆571Updated 4 years ago
• mikelove / awesome-multi-omics
  List of software packages for multi-omics analysis
  ☆818Updated 2 months ago
• mousepixels / sanbomics_scripts
  scripts and notebooks from sanbomics
  ☆426Updated 7 months ago
• crazyhottommy / scRNAseq-analysis-notes
  scRNAseq analysis notes from Ming Tang
  ☆717Updated 7 months ago
• hemberg-lab / scRNA.seq.course
  Analysis of single cell RNA-seq data course
  ☆676Updated 3 years ago
• pachterlab / BI-BE-CS-183-2023
  Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023
  ☆493Updated last year
• zqfang / GSEApy
  Gene Set Enrichment Analysis in Python
  ☆643Updated last month
• aertslab / pySCENIC
  pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…
  ☆522Updated 3 weeks ago
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆366Updated 6 months ago
• crazyhottommy / RNA-seq-analysis
  RNAseq analysis notes from Ming Tang
  ☆1,016Updated 3 years ago
• sqjin / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
  ☆709Updated last year
• owkin / PyDESeq2
  A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
  ☆659Updated last week
• saeyslab / nichenetr
  NicheNet: predict active ligand-target links between interacting cells
  ☆551Updated 2 weeks ago
• broadinstitute / infercnv
  Inferring CNV from Single-Cell RNA-Seq
  ☆625Updated 5 months ago
• jinworks / CellChat
  R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
  ☆429Updated 2 weeks ago
• omnideconv / immunedeconv
  A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution method…
  ☆498Updated last week
• chris-mcginnis-ucsf / DoubletFinder
  R package for detecting doublets in single-cell RNA sequencing data
  ☆482Updated 3 months ago
• immunogenomics / harmony
  Fast, sensitive and accurate integration of single-cell data with Harmony
  ☆580Updated 8 months ago
• Teichlab / scg_lib_structs
  Collections of library structure and sequence of popular single cell genomic methods
  ☆471Updated last month
• theislab / scvelo
  RNA Velocity generalized through dynamical modeling
  ☆451Updated 4 months ago
• agitter / single-cell-pseudotime
  An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
  ☆427Updated last month
• crazyhottommy / ChIP-seq-analysis
  ChIP-seq analysis notes from Ming Tang
  ☆809Updated 11 months ago
• zhanghao-njmu / SCP
  An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
  ☆525Updated last year
• ventolab / CellphoneDB
  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
  ☆409Updated last month
• 10XGenomics / cellranger
  10x Genomics Single Cell Analysis
  ☆424Updated 5 months ago
• scverse / scvi-tools
  Deep probabilistic analysis of single-cell and spatial omics data
  ☆1,411Updated last week