Alternatives and similar repositories for scdownstream:

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

• tavareshugo / tutorial_DESeq2_contrasts
  ☆58Updated 10 months ago
• andygxzeng / BoneMarrowMap
  A single cell RNA-seq reference map of human hematopoietic development in the bone marrow, with balanced representation of hematopoietic …
  ☆38Updated 4 months ago
• minoda-lab / universc
  UniverSC: a flexible cross-platform single-cell data processing pipeline
  ☆45Updated last year
• rpolicastro / scProportionTest
  ☆61Updated last year
• dozmorovlab / excluderanges
  Genomic coordinates of problematic genomic regions as GRanges
  ☆35Updated 3 months ago
• nf-core / spatialvi
  Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcri…
  ☆59Updated last week
• saezlab / transcriptutorial
  This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL
  ☆55Updated last year
• sandberg-lab / Smart-seq3
  Code and analysis pipeline for Smart-seq3 (Hagemann-Jensen et al. 2020).
  ☆51Updated 3 years ago
• PierreBSC / Viral-Track
  ☆57Updated 4 years ago
• vib-singlecell-nf / vsn-pipelines
  A repository of pipelines for single-cell data in Nextflow DSL2
  ☆75Updated last year
• KChen-lab / Monopogen
  SNV calling from single cell sequencing
  ☆93Updated 4 months ago
• liulab-dfci / RIMA_pipeline
  ☆78Updated last year
• AllonKleinLab / scrublet
  Detect doublets in single-cell RNA-seq data
  ☆36Updated 5 years ago
• single-cell-genetics / cellSNP
  Pileup biallelic SNPs from single-cell and bulk RNA-seq data
  ☆77Updated 2 years ago
• databio / awesome-atac-analysis
  Links to ATAC-seq analysis tools
  ☆63Updated 3 years ago
• yezhengSTAT / CUTTag_tutorial
  Tutorial Website
  ☆57Updated 4 years ago
• noush-joglekar / scisorseqr
  scisorseqr is an R-package for processing of single-cell long read data and analyzing differential isoform expression across any two cond…
  ☆37Updated 2 years ago
• kvittingseerup / IsoformSwitchAnalyzeR
  An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
  ☆111Updated last month
• chris-mcginnis-ucsf / MULTI-seq
  R implementation of MULTI-seq sample classification workflow
  ☆61Updated last year
• liulab-dfci / MAGeCK
  Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent gen…
  ☆28Updated 4 years ago
• wbaopaul / scATAC-pro
  A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
  ☆74Updated 2 weeks ago
• timoast / sinto
  Tools for single-cell data processing
  ☆122Updated 9 months ago
• CebolaLab / ATAC-seq
  Analysis pipeline for ATAC-seq data
  ☆48Updated last year
• sridnona / cb_sniffer
  mutation(barcode) caller for 10x single cell data
  ☆44Updated 4 years ago
• Hoohm / CITE-seq-Count
  A tool that allows to get UMI counts from a single cell protein assay
  ☆82Updated 7 months ago
• reskejak / ATAC-seq
  Basic workflow for ATAC-seq analysis
  ☆75Updated last year
• AmpliconSuite / AmpliconSuite-pipeline
  A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior …
  ☆63Updated 2 weeks ago
• carmonalab / scGate
  marker-based purification of cell types from single-cell RNA-seq datasets
  ☆106Updated last month
• tobiasrausch / ATACseq
  Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
  ☆75Updated last year
• rajewsky-lab / spacemake
  ☆41Updated this week