Alternatives and similar repositories for CSI-Microbes-identification

Users that are interested in CSI-Microbes-identification are comparing it to the libraries listed below

• FredHutch / Galeano-Nino-Bullman-Intratumoral-Microbiota_2022
  Analysis code used in Galeano Nino et al., Impact of Intratumoral Microbiota on Spatial and Cellular Heterogeneity in human cancer. 2022
  ☆38Updated last year
• wenweixiong / MARVEL
  ☆53Updated last year
• McGranahanLab / TcellExTRECT
  ☆48Updated last year
• ruppinlab / tcga-microbiome-prediction
  Predictive models and analysis of cancer prognosis and drug response using primary tumor microbial abundances derived from WGS and RNA-se…
  ☆18Updated last year
• stjude / ROSE
  ROSE: RANK ORDERING OF SUPER-ENHANCERS
  ☆62Updated 2 months ago
• noriakis / CBNplot
  Bayesian network plot for the enrichment analysis results
  ☆66Updated last year
• kerseviciute / aPEAR
  Enrichment Networks for Pathway Enrichment Analysis
  ☆66Updated 2 years ago
• liulab-dfci / RIMA_pipeline
  ☆89Updated 4 months ago
• ruppinlab / CSI-Microbes-analysis
  The code for running the analysis component of CSI-Microbe
  ☆12Updated 2 years ago
• yjzhang / split-seq-pipeline
  ☆23Updated 5 years ago
• gerstung-lab / MutationTimeR
  An R package to time somatic mutations
  ☆65Updated 5 years ago
• sjdlabgroup / SAHMI
  ☆88Updated last year
• BMILAB / scAPAtrap
  ☆25Updated 2 months ago
• VCCRI / Sierra
  Discover differential transcript usage from polyA-captured single cell RNA-seq data
  ☆53Updated 2 years ago
• lkmklsmn / MitoTrace
  ☆18Updated last year
• PierreBSC / Viral-Track
  ☆62Updated 5 years ago
• UPSUTER / GEMLI
  ☆32Updated 11 months ago
• Simon-Leonard / FlexDotPlot
  R package for Flexible dot plots
  ☆29Updated 3 years ago
• single-cell-genetics / cellSNP
  Pileup biallelic SNPs from single-cell and bulk RNA-seq data
  ☆81Updated 3 years ago
• EDePasquale / DoubletDecon
  A tool for removing doublets from single-cell RNA-seq data
  ☆75Updated 5 years ago
• ratschlab / pancanatlas_code_public
  Public repository containing research code for the TCGA PanCanAtlas Splicing project
  ☆42Updated 4 years ago
• PCAWG-11 / Heterogeneity
  Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
  ☆44Updated 4 years ago
• omicsCore / scTyper
  scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data
  ☆31Updated 3 years ago
• mbassalbioinformatics / CnRAP
  Analytical pipeline developed to anlayze Cut and Run data. Inspired by both Henikoff (SEACR) and Orkin (Cut&RunTools) lab pipelines.
  ☆19Updated 7 months ago
• MarioniLab / DropletUtils
  Clone of the Bioconductor repository for the DropletUtils package.
  ☆63Updated 4 months ago
• Moonerss / CIBERSORT
  ☆43Updated last month
• junjunlab / bulkPseudotime
  Pseudotime Analysis for Bulk Data
  ☆18Updated last year
• 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
• CebolaLab / CUTandTAG
  Analysis pipeline for CUT&TAG data
  ☆21Updated 5 years ago
• fmicompbio / monaLisa
  binned motif enrichment analysis and visualisation
  ☆43Updated 2 months ago