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scate

https://github.com/winnie09/scate

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
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    codemeta.json file
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    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
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    Committers with academic emails
    2 of 6 committers (33.3%) from academic institutions
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    Scientific vocabulary similarity
    Low similarity (15.1%) to scientific vocabulary

Keywords from Contributors

bioconductor-package grna-sequence immune-repertoire gene transcriptomics ontology sequencing genomics proteomics recount3
Last synced: 11 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: Winnie09
  • License: mit
  • Language: R
  • Default Branch: master
  • Size: 154 MB
Statistics
  • Stars: 1
  • Watchers: 4
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created about 6 years ago · Last pushed over 3 years ago

https://github.com/Winnie09/SCATE/blob/master/ 

SCATE: Single-cell ATAC-seq Signal Extraction and Enhancement
====

## Introductions
Single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) is
the state-of-the-art technology for analyzing genome-wide regulatory landscape in
single cells. Due to data sparsity and discreteness, analyzing scATAC-seq data is
challenging. Existing computational methods cannot accurately reconstruct
activities of individual cis-regulatory elements (CREs) in individual cells. We
present a new statistical framework, SCATE, that adaptively integrates
information from co-activated CREs, similar cells, and publicly available regulome
data to substantially increase the accuracy for estimating individual CRE
activities in single cell and rare cell subpopulations. 

## SCATE Installation

SCATE software can be installed via Github.
Users should have R installed on their computer before installing SCATE. R version needs to be at least 3.5.x or higher. R can be downloaded here: http://www.r-project.org/.

For Windows users, Rtools is also required to be installed. Rtools can be downloaded here: (https://cloud.r-project.org/bin/windows/Rtools/). For R version 3.5.x, Rtools35.exe is recommended. Use default settings to perform the installation.

For mac users, if there is any problem with installation problem, please try download and install clang-8.0.0.pkg from the following URL: https://cloud.r-project.org/bin/macosx/tools/clang-8.0.0.pkg

To install the latest version of SCATE package via Github, run following commands in R:
```{r }
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(c("GenomicAlignments","preprocessCore"))
if (!require("devtools"))
  install.packages("devtools")
devtools::install_github("zji90/SCATE")
```


If there is any problem with the installation process, please make sure you have R version at least 3.5.x and you have installed Rtools (Windows users) or clang (mac users). If the problem still occurs, please contact the author (see below)

## User Manual
Check the following page for PDF version of the user manual:
https://github.com/zji90/SCATE/raw/master/inst/doc/SCATE.pdf

Check below link for the R code of the user manual.

https://github.com/zji90/SCATE/blob/master/inst/doc/SCATE.R

## Citation 

Zhicheng Ji, Weiqiang Zhou, Wenpin Hou, Hongkai Ji, [*Single-cell ATAC-seq Signal Extraction and Enhancement with SCATE*](https://doi.org/10.1186/s13059-020-02075-3), Genome Biol 21, 161 (2020).

## Contact
Author: Zhicheng Ji, Weiqiang Zhou, Wenpin Hou, Hongkai Ji 

Report bugs and provide suggestions by sending email to:

Maintainer: Zhicheng Ji (zji4@jhu.edu), Wenpin Hou (whou10@jhu.edu)

Or open a new issue on this Github page

Owner

  • Name: Wenpin Hou
  • Login: Winnie09
  • Kind: user
  • Location: New York
  • Company: Columbia University

Assistant Professor, Dept of Biostatistics

GitHub Events

Total
Last Year

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 54
  • Total Committers: 6
  • Avg Commits per committer: 9.0
  • Development Distribution Score (DDS): 0.315
Past Year
  • Commits: 5
  • Committers: 3
  • Avg Commits per committer: 1.667
  • Development Distribution Score (DDS): 0.6
Top Committers
Name Email Commits
Wenpin Hou w****3@g****m 37
Nitesh Turaga n****a@g****m 8
Wenpin Hou w****u@g****l 4
J Wokaty j****y 2
J Wokaty j****y@s****u 2
Wenpin Hou w****0@j****u 1
Committer Domains (Top 20 + Academic)
jhu.edu: 1 sph.cuny.edu: 1

Issues and Pull Requests

Last synced: over 2 years ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Dependencies

DESCRIPTION cran
  • Rtsne * depends
  • SCATEData * depends
  • mclust * depends
  • parallel * depends
  • preprocessCore * depends
  • splines * depends
  • splines2 * depends
  • xgboost * depends
  • GenomicAlignments * imports
  • GenomicRanges * imports
  • stats * imports
  • utils * imports
  • BiocStyle * suggests
  • ggplot2 * suggests
  • knitr * suggests
  • rmarkdown * suggests