Alternatives and similar repositories for FootprintPipeline

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

• crazyhottommy / scCustomize
  Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
  ☆16Updated 3 years ago
• caleblareau / bap
  Bead-based single-cell atac processing
  ☆33Updated 3 years ago
• kundajelab / ataqc
  ☆17Updated 6 years ago
• GreenleafLab / NucleoATACR
  R package for reading in & working with NucleoATAC outputs
  ☆26Updated 6 years ago
• caleblareau / gchromVAR
  Cell type specific enrichments using finemapped variants and quantitative epigenetic data
  ☆45Updated last year
• ManchesterBioinference / IntegratingATAC-RNA-HiC
  scripts for the integrating ATAC-seq, RNA-seq and CHi-C paper
  ☆24Updated 2 years ago
• saezlab / footprints
  Analysis code for "Perturbation-response genes reveal signaling footprints in cancer gene expression"
  ☆20Updated 7 years ago
• ParkerLab / atactk
  A toolkit for working with ATAC-seq data.
  ☆24Updated last year
• neuhausi / single-cell-viewer
  R package to visualize scRNA sequencing data.
  ☆20Updated 3 years ago
• cole-trapnell-lab / monocle2-rge-paper
  Scripts needed to generate the figures for the Monocle 2 paper (Qiu et al, 2017)
  ☆29Updated 4 years ago
• yuchaojiang / SCALE
  Allele-Specific Expression by Single-Cell RNA Sequencing
  ☆28Updated 4 years ago
• bodegalab / irescue
  Uncertainty-aware quantification of Transposable Elements expression in scRNA-seq
  ☆17Updated 2 months 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
• BMILAB / scAPAtrap
  ☆21Updated last year
• crazyhottommy / scRNA-seq-workshop-Fall-2019
  Harvard FAS informatics scRNAseq workshop website
  ☆37Updated 5 years ago
• stjude / ChIPseqSpikeInFree
  A Spike-in Free ChIP-Seq Normalization Approach for Detecting Global Changes in Histone Modifications
  ☆33Updated 3 years ago
• bioinfo-biols / Code_for_circSC
  Analysis pipeline for our circSC manuscript
  ☆13Updated 3 years ago
• jw156605 / SingleSplice
  Algorithm for detecting alternative splicing in a population of single cells. See details in Welch et al., Nucleic Acids Research 2016: h…
  ☆21Updated 8 years ago
• ati-lz / HCA_Benchmarking
  This repository contains HCA Benchmarking codes
  ☆26Updated 5 years ago
• Morriseylab / scExtras
  ☆13Updated 11 months ago
• YiPeng-Gao / scDaPars
  Dynamic Analysis of Alternative Polyadenylation from single-cell RNA-seq (scDaPars)
  ☆15Updated 4 years ago
• TheJacksonLaboratory / BRCA-LRseq-pipeline
  Pipeline to analyze long-read mRNA isoforms and ORF products sequenced in breast cancer using PacBio Single-Molecule technology.
  ☆16Updated 3 years ago
• BUStools / BUS_notebooks_R
  R vignettes for processing BUS format single-cell RNA-seq files
  ☆20Updated 5 years ago
• statOmics / satuRn
  satuRn is a highly performant and scalable method for performing differential transcript usage analyses.
  ☆22Updated 2 years ago
• wanqingshao / TE_expression_in_scRNAseq
  ☆17Updated 4 years ago
• wzthu / esATAC
  Bioconductor package esATAC: an Easy-to-use Systematic pipeline for ATAC-seq data analysis
  ☆23Updated 2 years ago
• dbrg77 / plate_scATAC-seq
  A rapid and robust plate-based single cell ATAC-seq (scATAC-seq) method
  ☆43Updated 4 years ago
• eudoraleer / scasa
  SCASA: Single cell transcript quantification tool
  ☆21Updated last year
• ConesaLab / acorde
  Isoform co-usage networks from single-cell RNA-seq data
  ☆16Updated last year
• GreenleafLab / chromVARmotifs
  R package with motifs for use with chromVAR
  ☆28Updated 7 years ago