Alternatives and similar repositories for speckle:

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

• aet21 / EpiSCORE
  Epigenetic cell-type deconvolution from Single-Cell Omic Reference profiles
  ☆31Updated last year
• powellgenomicslab / DropletQC
  Nuclear fraction QC metric to detect empty droplets and damaged cells in scRNA-seq data
  ☆35Updated 3 years ago
• saezlab / CollecTRI
  Gene regulatory network containing signed transcription factor-target gene interactions
  ☆71Updated 10 months ago
• PoolLab / generecovery
  ☆29Updated last year
• wmacnair / psupertime
  psupertime is pseudotime ordering for single cell RNA-seq data with sequential labels
  ☆38Updated 2 years ago
• niaid / dsb
  Normalize CITEseq Data
  ☆65Updated 8 months ago
• lhe17 / nebula
  ☆35Updated last year
• MarioniLab / StabMap
  Mosaic single cell data integration using non-overlapping features
  ☆37Updated 2 years ago
• shenorrLabTRDF / cellAlign
  ☆38Updated 4 years ago
• oganm / homologene
  An r package that works as a wrapper to homologene
  ☆42Updated last year
• jlaffy / infercna
  Infer Copy Number Alterations and Clonality in (Single-Cell) RNA-Seq Data
  ☆32Updated last year
• KlugerLab / DAseq
  ☆39Updated 3 years ago
• ZJUFanLab / CellTalkDB
  A manually curated database of literature-supported ligand-receptor interactions in human and mouse
  ☆29Updated 8 months ago
• atakanekiz / CIPR-Package
  Cluster Identity Predictor (R package implementation)
  ☆20Updated 3 years ago
• Oshlack / speckle
  R package for specialised analysis of single cell data
  ☆37Updated 2 years ago
• FelixTheStudent / cellpypes
  Cell type pipes for R
  ☆51Updated last year
• VCCRI / Sierra
  Discover differential transcript usage from polyA-captured single cell RNA-seq data
  ☆50Updated last year
• NBISweden / single-cell_sib_scilifelab
  SIB/Scilifelab autumn school in single cell omics 2019.
  ☆22Updated 5 years ago
• HectorRDB / condiments
  Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression
  ☆26Updated 3 months ago
• omnideconv / spacedeconv
  A unified interface to spatial transcriptomics deconvolution tools
  ☆40Updated last week
• zdebruine / singlet
  Single-cell analysis with non-negative matrix factorization
  ☆44Updated 4 months ago
• single-cell-genetics / XClone
  Detection of allele-specific subclonal copy number alterations from single-cell transcriptomic data.
  ☆36Updated this week
• UPSUTER / GEMLI
  ☆30Updated last month
• zijianni / SpotClean
  R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data
  ☆31Updated 9 months ago
• CFeregrino / scWGCNA
  scWGCNA
  ☆56Updated 2 years ago
• swaruplabUCI / ArchRtoSignac
  An R package performing object conversion from ArchRProject (ArchR) to Signac SeuratObject (Signac)
  ☆35Updated 6 months ago
• wmacnair / SampleQC
  Robust, multivariate, multi-sample, multi-celltype QC for single cell RNA-seq data
  ☆36Updated 2 years ago
• morris-lab / CellTagR
  This repository contains the CellTag data analysis R package to support clone calling and lineage reconstruction.
  ☆21Updated 2 years ago
• single-cell-genetics / cardelino
  Clone identification from single-cell data
  ☆61Updated 2 years ago
• colomemaria / epiAneufinder
  R package to detect breakpoints and assign somies to scATAC-seq data
  ☆34Updated last week