Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/alleninstitute/patchseqtools

QC and cell type assignment for patch-seq transcriptomics data

https://github.com/alleninstitute/patchseqtools

Science Score: 33.0%

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
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: sciencedirect.com, nature.com
  • ✓
    Committers with academic emails
    2 of 3 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

QC and cell type assignment for patch-seq transcriptomics data

Basic Info
  • Host: GitHub
  • Owner: AllenInstitute
  • License: other
  • Language: HTML
  • Default Branch: master
  • Size: 7.37 MB
Statistics
  • Stars: 20
  • Watchers: 6
  • Forks: 4
  • Open Issues: 0
  • Releases: 1
Created almost 8 years ago · Last pushed about 2 years ago
Metadata Files
Readme License

README.md

Allen Institute Patch-seq documents and tools

Patch-seq is powerful technique that allows for multimodal characterization of individual neurons – electrophysiological, morphological and transcriptomic. At the Allen Institute we have optimized this technique to efficiently collect high-quality data. On this GitHub repo we provide links to the manuscript describing this optimized technique and associated data, a detailed protocol, Allen Institute manuscripts that have utilized this technique, and links to Allen Institute resources and software. In addition, this repo includes an R package of Patch-seq tools for quality control and cell typing of Patch-seq cells.

Patch-seq detailed protocol on protocols.io

https://www.protocols.io/view/patch-seq-recording-and-extraction-detailed-protoc-bw6gphbw

Scaled, high fidelity electrophysiological, morphological, and transcriptomic cell characterization

https://elifesciences.org/articles/65482

Multichannel Igor Electrophysiology Suite (MIES) Github repo

https://github.com/AllenInstitute/MIES

Allen Institute Patch-seq papers

Mouse Visual Cortex https://www.sciencedirect.com/science/article/pii/S009286742031254X

Human L2/3 - https://www.nature.com/articles/s41586-021-03813-8

Allen Institute cell types web products

Morpho-Electric database http://celltypes.brain-map.org/

Single-cell RNA-seq database https://portal.brain-map.org/atlases-and-data/rnaseq

Patch-Seq database of cells in mouse VISp is now available on Allen Brain Map.

Patch-seq tools

R functions for gene selection and analysis of Patch-seq data.

patchseqtools includes several functions that are used for quality control and cell typing of Patch-seq cells at the Allen Institute. Many of these functions are wrappers for functions from other libraries (see below) and we enourage proper citation of relevant tools when using those functions.

Specific topics include:
1. Assigning quality scores to each cell (mostly wrapper functions for https://github.com/PavlidisLab/patchSeqQC)
2. Cell type clustering using CCA (mostly wrapper functions for https://satijalab.org/seurat/Seurat_AlignmentTutorial.html)

Installation

devtools::install_github("AllenInstitute/patchseqtools")

Library use cases

No vignettes currently available.

License

The license for this package is available on Github at: https://github.com/AllenInstitute/patchseqtools/blob/master/LICENSE

Level of Support

We are not planning to update the R library component of this repo unless bugs are found. We may make occasional updates to other components of the repository with no fixed schedule. However, we welcome community input through both issues and pull requests.

Contribution Agreement

If you contribute code to this repository through pull requests or other mechanisms, you are subject to the Allen Institute Contribution Agreement, which is available in full at: https://github.com/AllenInstitute/patchseqtools/blob/master/CONTRIBUTION

Owner

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

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

GitHub Events

Total
  • Watch event: 5
  • Fork event: 1
Last Year
  • Watch event: 5
  • Fork event: 1

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 36
  • Total Committers: 3
  • Avg Commits per committer: 12.0
  • Development Distribution Score (DDS): 0.556
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
jeremymiller j****m@a****g 16
leebrianr b****e@a****g 10
Agata Budzillo a****o@g****m 10
Committer Domains (Top 20 + Academic)
alleninstitute.org: 2

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 1
  • Total pull requests: 0
  • Average time to close issues: 8 minutes
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 3.0
  • 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
View more stats
Top Authors
Issue Authors
  • stripathy (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Dependencies

DESCRIPTION cran
  • Rtsne >= 0.13 imports
  • dendextend >= 1.7.0 imports
  • ggplot2 >= 2.2.1 imports
  • gplots >= 3.0.1 imports
  • matrixStats >= 0.53.1 imports
  • pdist >= 1.2 imports