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
  ☆37Updated last year
• knightlab-analyses / mycobiome
  Pan-cancer mycobiome atlas
  ☆27Updated 2 years ago
• ruppinlab / CSI-Microbes-analysis
  The code for running the analysis component of CSI-Microbe
  ☆12Updated last year
• liulab-dfci / RIMA_pipeline
  ☆82Updated last year
• noriakis / CBNplot
  Bayesian network plot for the enrichment analysis results
  ☆64Updated 9 months ago
• tushiqi / MAnorm2
  MAnorm2 for Normalizing and Comparing ChIP-seq Samples
  ☆33Updated 2 years ago
• wenweixiong / MARVEL
  ☆49Updated 11 months ago
• ggjlab / scHCL
  ☆47Updated 5 years ago
• minoda-lab / universc
  UniverSC: a flexible cross-platform single-cell data processing pipeline
  ☆45Updated last year
• McGranahanLab / TcellExTRECT
  ☆47Updated 6 months ago
• sridnona / cb_sniffer
  mutation(barcode) caller for 10x single cell data
  ☆45Updated 5 years ago
• wbaopaul / scATAC-pro
  A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
  ☆76Updated 4 months ago
• aertslab / SCopeLoomR
  R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters an…
  ☆42Updated 3 years ago
• UPSUTER / GEMLI
  ☆32Updated 5 months ago
• sjdlabgroup / SAHMI
  ☆82Updated 10 months ago
• omicsCore / scTyper
  scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data
  ☆30Updated 2 years ago
• sandberg-lab / Smart-seq3
  Code and analysis pipeline for Smart-seq3 (Hagemann-Jensen et al. 2020).
  ☆52Updated 3 years ago
• PCAWG-11 / Heterogeneity
  Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
  ☆43Updated 4 years ago
• VCCRI / Sierra
  Discover differential transcript usage from polyA-captured single cell RNA-seq data
  ☆51Updated 2 years ago
• 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…
  ☆17Updated 8 months ago
• gerstung-lab / MutationTimeR
  An R package to time somatic mutations
  ☆62Updated 4 years ago
• BMILAB / scAPAtrap
  ☆22Updated last year
• NKI-GCF / XenofilteR
  Filtering of PDX samples for mouse derived reads
  ☆28Updated 2 years ago
• yjzhang / split-seq-pipeline
  ☆22Updated 5 years ago
• ElkonLab / scAPA
  This is a package and a shell script for alternative polyadenylation (APA) analysis of 3' tag single-cell RNA-seq data.
  ☆21Updated 3 years ago
• single-cell-genetics / cellSNP
  Pileup biallelic SNPs from single-cell and bulk RNA-seq data
  ☆79Updated 3 years ago
• huangyh09 / brie
  BRIE: Bayesian Regression for Isoform Estimate in Single Cells
  ☆42Updated last year
• amf71 / cloneMap
  An R package to plot maps of clone distributions in somatic evolution
  ☆17Updated last year
• ysuzukilab / Cibersortx
  Repository for Cibersortx
  ☆61Updated 4 years ago
• prabhakarlab / DUBStepR
  Correlation-Based Feature Selection for Single-Cell RNA Sequencing Data
  ☆19Updated 2 years ago