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Open Source Science

https://github.com/alleninstitute/scrattch.mapping

Genearlized mapping scripts for RNA-seq and Patch-seq data

https://github.com/alleninstitute/scrattch.mapping

Science Score: 36.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    4 of 6 committers (66.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.2%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Genearlized mapping scripts for RNA-seq and Patch-seq data

Basic Info
  • Host: GitHub
  • Owner: AllenInstitute
  • Language: R
  • Default Branch: main
  • Size: 4.12 MB
Statistics
  • Stars: 14
  • Watchers: 5
  • Forks: 2
  • Open Issues: 9
  • Releases: 7
Created over 3 years ago · Last pushed about 1 year ago
Metadata Files
Readme

README.md

scrattch.mapping

Generalized mapping scripts for RNA-seq, Patch-seq or any gene expression data. Assumes that you have built an Allen Institute Taxonomy (AIT) object with scrattch.taxonomy.

Documentation

You can find a detail description of all scrattch.mapping functions here: Documentation

Update notes are here: Versions

Installation

Using docker (recommended)

We have setup a docker environment for scrattch.taxonomy, scrattch.mapping, and scrattch.patchseq that contains all the required dependencies and the current version of all scrattch packages. See the readme for the parent scrattch package for the most up-to-date docker information.

Directly from GitHub (strongly discouraged)

While we advise using the provided docker, you can also install scrattch.mapping directly from GitHub as follows:

devtools::install_github("AllenInstitute/scrattch.mapping")

This strategy might not work due to complicated dependencies. Also note that doMC may need to be installed manually from HERE if you use Windows. Vignettes are provided below.

Usage examples

  1. Run Flat, Tree, and Seurat taxonomy mapping This examples shows how to use scrattch.mapping for standard taxonomy mapping.
  2. Mapping to HMBA Basal Ganglia AIT This tutorial shows how to map against the HMBA Human and Macaque Basal Ganglia consensus taxonomies.

Reporting issues

If you run into any issues, please let Nelson and Jeremy know or create a new issue in the 'Issues' tab above.

Owner

  • Name: Allen Institute
  • Login: AllenInstitute
  • Kind: organization
  • Location: Seattle, WA

Please visit http://alleninstitute.github.io/ for more information.

GitHub Events

Total
  • Create event: 8
  • Release event: 1
  • Issues event: 2
  • Watch event: 5
  • Issue comment event: 3
  • Push event: 40
  • Pull request event: 17
  • Fork event: 1
Last Year
  • Create event: 8
  • Release event: 1
  • Issues event: 2
  • Watch event: 5
  • Issue comment event: 3
  • Push event: 40
  • Pull request event: 17
  • Fork event: 1

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 230
  • Total Committers: 6
  • Avg Commits per committer: 38.333
  • Development Distribution Score (DDS): 0.57
Past Year
  • Commits: 51
  • Committers: 4
  • Avg Commits per committer: 12.75
  • Development Distribution Score (DDS): 0.608
Top Committers
Name Email Commits
Nelson Johansen n****n@u****u 99
jeremymiller j****m@a****g 84
inkarkapen i****n@g****m 24
Changkyu Lee c****l@a****g 11
Inkar Kapen i****n@i****g 9
ikapen-alleninst 1****t 3
Committer Domains (Top 20 + Academic)
alleninstitute.org: 2 ibs-hct-ux3.corp.alleninstitute.org: 1 ucdavis.edu: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 15
  • Total pull requests: 59
  • Average time to close issues: 13 days
  • Average time to close pull requests: 4 days
  • Total issue authors: 7
  • Total pull request authors: 5
  • Average comments per issue: 2.0
  • Average comments per pull request: 0.1
  • Merged pull requests: 54
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 17
  • Average time to close issues: N/A
  • Average time to close pull requests: 3 days
  • Issue authors: 3
  • Pull request authors: 3
  • Average comments per issue: 0.33
  • Average comments per pull request: 0.0
  • Merged pull requests: 16
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • UCDNJJ (4)
  • xpliu16 (4)
  • scseeman (3)
  • meghanaturner (1)
  • cvanvelt (1)
  • jeremymiller (1)
Pull Request Authors
  • UCDNJJ (24)
  • inkarkapen (23)
  • jeremymiller (17)
  • leechangkyu (4)
  • ikapen-alleninst (3)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

DESCRIPTION cran
  • BiocNeighbors * depends
  • Matrix * depends
  • MatrixGenerics * depends
  • RANN * depends
  • Seurat * depends
  • anndata * depends
  • arrow * depends
  • cowplot * depends
  • dendextend * depends
  • dplyr * depends
  • feather * depends
  • foreach * depends
  • mfishtools * depends
  • patchSeqQC * depends
  • patchseqtools * depends
  • pvclust * depends
  • scrattch.bigcat * depends
  • scrattch.hicat * depends
  • scrattch.io * depends
  • scrattch.taxonomy * depends
  • scrattch.vis * depends
  • tibble * depends
  • umap * depends
  • viridis * depends
  • doMC * suggests
  • future * suggests
  • knitr * suggests
  • parallel * suggests
  • rmarkdown * suggests
  • testthat * suggests
Dockerfile docker
  • rocker/tidyverse 4.2 build