Alternatives and similar repositories for EPEE

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

• yuchaojiang / SCALE
  Allele-Specific Expression by Single-Cell RNA Sequencing
  ☆28Updated 4 years ago
• Simon-Coetzee / motifBreakR
  A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.
  ☆29Updated 10 months ago
• cfce / chilin
  ChIP-seq DC and QC Pipeline
  ☆34Updated 4 years ago
• caleblareau / bap
  Bead-based single-cell atac processing
  ☆33Updated 3 years ago
• liulab-dfci / lisa
  epigenome analysis to rank transcription factors
  ☆13Updated 5 years ago
• Dowell-Lab / DAStk
  Differential ATAC-seq toolkit
  ☆27Updated last year
• GreenleafLab / NucleoATACR
  R package for reading in & working with NucleoATAC outputs
  ☆26Updated 6 years ago
• jgamache014 / snRNA-seq-workflow
  Human brain, >200,000 nuclei
  ☆24Updated 3 years ago
• ParkerLab / atactk
  A toolkit for working with ATAC-seq data.
  ☆24Updated 11 months ago
• satijalab / scChromHMM
  🧬 🦀 A fast and efficient tool to perform a genome wide Single cell Chromatin State Analysis using multimodal histone modification data.…
  ☆28Updated 3 years ago
• GreenleafLab / chromVARmotifs
  R package with motifs for use with chromVAR
  ☆28Updated 7 years ago
• shendurelab / single-cell-ko-screens
  Repository containing all code for secondary analysis in the manuscript "On the design of CRISPR-based single cell molecular screens", Hi…
  ☆26Updated 3 years ago
• linnarsson-lab / cytograph
  Algorithms for single-cell analysis
  ☆29Updated 3 years ago
• pachterlab / scRNA-Seq-TCC-prep
  Preprocessing of single-cell RNA-Seq (deprecated)
  ☆62Updated 5 years ago
• vanallenlab / retained-intron-neoantigen-pipeline
  Pipeline to call neoantigens from intron retention events derived from RNA-Seq data.
  ☆28Updated 4 years ago
• fmicompbio / monaLisa
  binned motif enrichment analysis and visualisation
  ☆40Updated last month
• cole-trapnell-lab / pseudospace
  ☆12Updated 5 years ago
• greenelab / tad_pathways_pipeline
  Pipeline to implement a "TAD_Pathways" analysis. Discover candidate genes based on association signals in TADs
  ☆11Updated 5 years ago
• naikai / sake
  sake
  ☆27Updated 2 years ago
• de-Boer-Lab / MAUDE
  Mean Alterations Using Discrete Expression
  ☆14Updated last year
• Teichlab / GPfates
  ☆19Updated 7 years ago
• mikelove / zinbwave-deseq2
  Workflow for ZINB-WaVE + DESeq2 intergration for single-cell RNA-seq
  ☆31Updated 4 years ago
• edsgard / scphaser
  R package for haplotype phasing using single-cell RNA-seq data
  ☆13Updated 7 years ago
• klarman-cell-observatory / scSVA
  Single-cell Scalable Visualization and Analytics
  ☆25Updated 6 years ago
• greenelab / hgsc_subtypes
  Two or three subtypes of high grade serous ovarian cancer subtypes fit data from different populations better than four
  ☆12Updated 6 years ago
• broadinstitute / single_cell_classification
  Methods to use SNPs or gene expression to classify single cell RNAseq to reference profiles
  ☆29Updated 5 years ago
• juliaolivieri / SpliZ_pipeline
  Code to calculate the Splicing Z Score (SpliZ) for single cell RNA-seq splicing analysis
  ☆33Updated 3 years ago
• broadinstitute / mix_seq_ms
  Code associated with MIX-seq manuscript
  ☆15Updated 4 years ago
• dcalderon / rolypoly
  Method for identifying trait-relevant gene annotations from GWAS summary statistics.
  ☆18Updated 2 years ago
• yiplabcuhk / JEME
  JEME method for predicting enhancer targets
  ☆11Updated 7 years ago