Alternatives and similar repositories for sake:

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

• GreenleafLab / NucleoATACR
  R package for reading in & working with NucleoATAC outputs
  ☆26Updated 6 years ago
• Neurosurgery-Brain-Tumor-Center-DiazLab / CONICS
  CONICS: COpy-Number analysis In single-Cell RNA-Sequencing
  ☆74Updated 2 years ago
• yuchaojiang / SCALE
  Allele-Specific Expression by Single-Cell RNA Sequencing
  ☆28Updated 4 years ago
• ParkerLab / atactk
  A toolkit for working with ATAC-seq data.
  ☆24Updated 10 months ago
• caleblareau / bap
  Bead-based single-cell atac processing
  ☆33Updated 3 years ago
• BUStools / BUS_notebooks_python
  ☆23Updated 5 years ago
• r3fang / snATAC
  <<------ Use SnapATAC!!
  ☆25Updated 6 years ago
• pachterlab / scRNA-Seq-TCC-prep
  Preprocessing of single-cell RNA-Seq (deprecated)
  ☆62Updated 5 years ago
• kundajelab / ataqc
  ☆16Updated 6 years ago
• jon-xu / scSplit
  Genotype-free demultiplexing of pooled single-cell RNA-Seq, using a hidden state model for identifying genetically distinct samples withi…
  ☆41Updated 2 years ago
• crazyhottommy / scATACutils
  R/Bioconductor package for working with 10x scATACseq data
  ☆39Updated last year
• wzthu / esATAC
  Bioconductor package esATAC: an Easy-to-use Systematic pipeline for ATAC-seq data analysis
  ☆23Updated 2 years ago
• dan-landau / IronThrone-GoT
  processes GoT amplicon data and generates a table of metrics
  ☆29Updated 2 years ago
• YeoLab / singlecell_pnm
  Code and figures accompanying the paper, "Single-cell alternative splicing analysis with Expedition reveals splicing dynamics during neu…
  ☆20Updated 7 years ago
• dbrg77 / plate_scATAC-seq
  A rapid and robust plate-based single cell ATAC-seq (scATAC-seq) method
  ☆43Updated 4 years ago
• cfce / chilin
  ChIP-seq DC and QC Pipeline
  ☆34Updated 4 years ago
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆42Updated 3 years ago
• epigen / crop-seq
  Data analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)
  ☆30Updated 7 years ago
• adamh-broad / single_cell_intestine
  R code for single-cell analysis of intestinal epithelial cells
  ☆22Updated 7 years ago
• dphansti / mango
  chia pet analysis software
  ☆25Updated 6 years ago
• caleblareau / gchromVAR
  Cell type specific enrichments using finemapped variants and quantitative epigenetic data
  ☆45Updated last year
• AllenWLynch / lisa
  ☆16Updated last year
• ncbi / scPopCorn
  A python tool to do comparative analysis of mulitple single cell datasets.
  ☆22Updated 5 years ago
• JEFworks / liger
  Lightweight Iterative Gene set Enrichment in R
  ☆56Updated 7 months ago
• statgen / popscle
  A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and au…
  ☆49Updated 4 years ago
• bvieth / scRNA-seq-pipelines
  Compendium to "A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines"
  ☆54Updated 4 years ago
• shawnzhangyx / PePr
  a peak-calling and differential analysis tool for replicated ChIP-Seq data
  ☆37Updated 2 years ago
• biobenkj / compartmap
  Reconstruction of higher order chromatin from scRNA-seq and scATAC-seq
  ☆14Updated this week
• daler / chromhmm-tools
  Helpers for working with ChromHMM (http://compbio.mit.edu/ChromHMM/)
  ☆17Updated 7 years ago
• SingleCellTranscriptomics / ISMB2018_SingleCellTranscriptomeTutorial
  See: https://www.iscb.org/ismb2018/3511#am1
  ☆18Updated 6 years ago