Alternatives and similar repositories for bulk_RNA_seq

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

• Castelo-Branco-lab / scCut-Tag_2020
  Code required to reproduce analysis of the single cell Cut and Tag data in the resource paper (Bartosovic et. al., 2020)
  ☆13Updated 4 years ago
• GuanLab / FastClone_GuanLab
  ☆15Updated 4 years ago
• kundajelab / ataqc
  ☆17Updated 6 years ago
• JunyueC / sci-fate_analysis
  Downstream analysis script for sci-fate (TF-gene linkage analysis / cell linkage analysis)
  ☆24Updated 5 years ago
• XiDsLab / scFusion
  ☆21Updated 3 years ago
• EskelandLab / ShinyArchRUiO
  ☆19Updated last month
• secrierlab / EMT
  This repository contains code for the evaluation of epithelial-to-mesenchymal transition states in cancer.
  ☆13Updated 2 years ago
• navinlabcode / copykit
  Toolkit for single-cell copy number analysis
  ☆24Updated last month
• sridnona / cb_sniffer
  mutation(barcode) caller for 10x single cell data
  ☆45Updated 5 years ago
• Dingpw / Endothelial-Cell-Heterogeneity-and-Microglia-Regulons-Revealed-by-A-Pig-Cell-Landscape-at-Single-cel
  ☆15Updated 2 years ago
• vari-bbc / rnaseq_workflow
  snakemake workflow for bulk RNA-seq workflow using STAR-edgeR
  ☆11Updated last month
• bvieth / scRNA-seq-pipelines
  Compendium to "A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines"
  ☆54Updated 4 years ago
• lanagarmire / SSrGE
  ☆34Updated 6 years ago
• JunyueC / sci-RNA-seq3_pipeline
  Processing pipeline scripts for sci-RNA-seq3 (bash, R, python)
  ☆43Updated 4 years ago
• buenrostrolab / dscATAC_analysis_code
  Analysis repository for "Droplet-based combinatorial indexing for massive scale single-cell epigenomics"
  ☆11Updated 5 years ago
• nasqar / deseq2shiny
  a web-based R shiny application that wraps DESeq2 R package
  ☆14Updated 5 years ago
• stjude / ROSE
  ROSE: RANK ORDERING OF SUPER-ENHANCERS
  ☆51Updated last year
• tushiqi / MAnorm2
  MAnorm2 for Normalizing and Comparing ChIP-seq Samples
  ☆32Updated 2 years ago
• r3fang / snATAC
  <<------ Use SnapATAC!!
  ☆25Updated 6 years ago
• single-cell-genetics / cellSNP
  Pileup biallelic SNPs from single-cell and bulk RNA-seq data
  ☆79Updated 3 years ago
• WRui / Post_Implantation
  ☆27Updated 4 years ago
• CostaLab / scrna_seurat_pipeline
  comprehensive analysis of single-cell transcriptomics data
  ☆24Updated 5 months ago
• McGranahanLab / TcellExTRECT
  ☆47Updated 7 months ago
• huangyh09 / brie
  BRIE: Bayesian Regression for Isoform Estimate in Single Cells
  ☆42Updated last year
• statgen / popscle
  A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and au…
  ☆56Updated 4 years ago
• bioinfo-biols / Code_for_circSC
  Analysis pipeline for our circSC manuscript
  ☆13Updated 3 years ago
• dibbelab / gficf
  An R implementation of the Gene Frequency - Inverse Cell Frequency method for single cell data normalization
  ☆15Updated 2 years ago
• caleblareau / singlecell_bloodtraits
  Data/analysis repository for "Interrogation of human hematopoiesis..." paper
  ☆20Updated 6 years ago
• ay-lab / ATACProc
  ATAC-seq processing pipeline
  ☆33Updated 3 years ago
• UCSF-DSOS / scRNA_seq
  scRNA seq analysis using Seurat V3
  ☆13Updated 4 years ago