muscat

Multi-sample multi-group scRNA-seq analysis tools

https://github.com/helenalc/muscat

Science Score: 49.0%

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Found 6 DOI reference(s) in README
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4 of 15 committers (26.7%) from academic institutions
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Low similarity (11.0%) to scientific vocabulary

Keywords from Contributors

bioconductor-package bioconductor bioinformatics mass-spectrometry rnaseq recount junction illumina human gene

Last synced: 6 months ago · JSON representation

Repository

Multi-sample multi-group scRNA-seq analysis tools

Basic Info

Host: GitHub
Owner: HelenaLC
Language: R
Default Branch: main
Homepage:
Size: 22.5 MB

Statistics

Stars: 198
Watchers: 14
Forks: 35
Open Issues: 39
Releases: 0

Created over 7 years ago · Last pushed 10 months ago

Metadata Files

Readme Changelog

README.md

muscat (Multi-sample **multi-group scRNA-seq analysis tools )**

...provides methods for Differential State (DS) analyses in scRNA-seq data
with multiple samples, groups, and (cell)-subpopulations, as elaborated in:

Crowell HL, Soneson C*, Germain P-L*,
Calini D, Collin L, Raposo C, Malhotra D & Robinson MD:
"muscat detects subpopulation-specific state transitions from
multi-sample multi-condition single-cell transcriptomics data"
Nature Communications 11, 6077 (2020)
DOI: 10.1038/s41467-020-19894-4

*These authors contributed equally.

installation

muscat is available through Bioconductor, and can be installed using the following commands:

r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("muscat")

quick guide

Let sce be a SingleCellExperiment object with cell metadata (colData) columns

"sample_id" specifying unique sample identifiers (e.g., PeterPan1, Nautilus7, ...)
"group_id" specifying each sample's experimental condition (e.g., reference/stimulated, healthy/diseased, ...)
"cluster_id" specifying subpopulation (cluster) assignments (e.g., B cells, dendritic cells, ...)

Aggregation-based methods come down to the following simple commands:

```r

compute pseudobulks (sum of counts)

pb <- aggregateData(sce, assay = "counts", fun = "sum", by = c("clusterid", "sampleid"))

run pseudobulk (aggregation-based) DS analysis

ds_pb <- pbDS(pb, method = "edgeR") ```

Mixed models can be run directly on cell-level measurements, e.g.:

r ds_mm <- mmDS(sce, method = "dream")

For details, please see the package vignettes.

differential detection

muscat also supports testing for differential detection as proposed in

Gilis J, Perin L, Malfait M, Van den Berge K,
Assefa AT, Verbist B, Risso D, and Clement L:
Differential detection workflows for
multi-sample single-cell RNA-seq data.
bioRxiv (2023). DOI: 10.1101/2023.12.17.572043

Key alterations to the commands above are highlighted below (!!!), however, we recommend users consult the corresponding publication and package vignette for more details.

```r

sum binarized counts

pb <- aggregateData(sce, assay = "counts", fun = "num.detected", # !!! by = c("clusterid", "sampleid"))

test for differential detection

dd <- pbDD(pb) # or.. dd <- pbDS(pb, method = "DD") ```

Owner

Name: Helena L. Crowell
Login: HelenaLC
Kind: user
Location: University of Zurich, Switzerland

Website: https://helenalc.github.io
Repositories: 7
Profile: https://github.com/HelenaLC

GitHub Events

Total

Issues event: 6
Watch event: 35
Delete event: 1
Issue comment event: 11
Push event: 16
Pull request event: 3
Fork event: 2
Create event: 3

Last Year

Issues event: 6
Watch event: 35
Delete event: 1
Issue comment event: 11
Push event: 16
Pull request event: 3
Fork event: 2
Create event: 3

Committers

Last synced: 10 months ago

All Time

Total Commits: 574
Total Committers: 15
Avg Commits per committer: 38.267
Development Distribution Score (DDS): 0.235

Past Year

Commits: 36
Committers: 5
Avg Commits per committer: 7.2
Development Distribution Score (DDS): 0.167

Top Committers

Name	Email	Commits
HelenaLC	h**a@c**u	439
HelenaLC	h**l@u**h	52
Helena Lucia Crowell	h**c@H**l	28
Pierre-Luc Germain	p**n@g**m	15
Nitesh Turaga	n**a@g**m	12
J Wokaty	j**y@s**u	10
Charlotte Soneson	c**n@g**m	4
Thony	t**s@h**m	3
Milan Malfait	m**4@g**m	3
Helena L. Crowell	c**h@s**h	2
Jeroen Gilis	g**s@c**e	2
Hervé Pagès	h**b@g**m	1
HelenaLC	h**a@c**u	1
Mark Robinson	m**n@i**h	1
A Wokaty	a**y@s**u	1

Committer Domains (Top 20 + Academic)

sph.cuny.edu: 2 imls.uzh.ch: 1 crowell.eu: 1 chalmers.se: 1 student.ethz.ch: 1 uzh.ch: 1 crowells.eu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 126
Total pull requests: 21
Average time to close issues: about 1 month
Average time to close pull requests: 11 days
Total issue authors: 86
Total pull request authors: 13
Average comments per issue: 2.67
Average comments per pull request: 0.67
Merged pull requests: 9
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 4
Pull requests: 5
Average time to close issues: about 3 hours
Average time to close pull requests: 19 days
Issue authors: 4
Pull request authors: 2
Average comments per issue: 1.25
Average comments per pull request: 0.6
Merged pull requests: 3
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

yuyingxie (10)
AnjaliC4 (5)
bassanio (5)
wmacnair (4)
Nayrouz109 (3)
wanghao98 (3)
priyamnarain (3)
HelenaLC (3)
lindsaynhayes (3)
milanmlft (2)
AnaBVA (2)
crazyhottommy (2)
BingbingYuan (2)
cakeinspace (2)
ismailelshimy (2)

Pull Request Authors

plger (5)
ansonrel (4)
jgilis (2)
markrobinsonuzh (2)
dbdimitrov (1)
XikunHan (1)
wmacnair (1)
HelenaLC (1)
markziemann (1)
molecules (1)
federicomarini (1)
milanmlft (1)
lpantano (1)

Top Labels

Issue Labels

enhancement (3) documentation (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- bioconductor 35,854 total

Total dependent packages: 1
Total dependent repositories: 0
Total versions: 6
Total maintainers: 1

bioconductor.org: muscat

Multi-sample multi-group scRNA-seq data analysis tools

Homepage: https://github.com/HelenaLC/muscat
Documentation: https://bioconductor.org/packages/release/bioc/vignettes/muscat/inst/doc/muscat.pdf
License: GPL-3
Latest release: 1.22.0
published 10 months ago

Versions: 6
Dependent Packages: 1
Dependent Repositories: 0
Downloads: 35,854 Total

Rankings

Dependent repos count: 0.0%

Dependent packages count: 0.0%

Stargazers count: 1.3%

Forks count: 1.4%

Average: 9.7%

Downloads: 46.1%

Maintainers (1)

helena@crowell.eu

Last synced: 7 months ago

Dependencies

DESCRIPTION cran

R >= 4.2 depends
BiocParallel * imports
ComplexHeatmap * imports
DESeq2 * imports
Matrix * imports
S4Vectors * imports
SingleCellExperiment * imports
SummarizedExperiment * imports
blme * imports
data.table * imports
dplyr * imports
edgeR * imports
ggplot2 * imports
glmmTMB * imports
grDevices * imports
grid * imports
limma * imports
lme4 * imports
lmerTest * imports
matrixStats * imports
methods * imports
progress * imports
purrr * imports
scales * imports
scater * imports
sctransform * imports
scuttle * imports
stats * imports
variancePartition * imports
viridis * imports
BiocStyle * suggests
ExperimentHub * suggests
RColorBrewer * suggests
UpSetR * suggests
countsimQC * suggests
cowplot * suggests
iCOBRA * suggests
knitr * suggests
phylogram * suggests
reshape2 * suggests
rmarkdown * suggests
statmod * suggests
testthat * suggests

.github/workflows/check-bioc.yml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/upload-artifact master composite
docker/build-push-action v1 composite
r-lib/actions/setup-pandoc master composite
r-lib/actions/setup-r master composite