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https://github.com/broadinstitute/drop-seq

Java tools for analyzing Drop-seq data

https://github.com/broadinstitute/drop-seq

Science Score: 26.0%

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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    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
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    Academic publication links
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    Scientific vocabulary similarity
    Low similarity (10.4%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Java tools for analyzing Drop-seq data

Basic Info
  • Host: GitHub
  • Owner: broadinstitute
  • License: mit
  • Language: Java
  • Default Branch: master
  • Size: 250 MB
Statistics
  • Stars: 129
  • Watchers: 17
  • Forks: 35
  • Open Issues: 16
  • Releases: 16
Created over 8 years ago · Last pushed 12 months ago
Metadata Files
Readme License

README.md

Drop-seq

Java and R tools for analyzing Drop-seq data

Drop-seq questions may be directed to dropseq@gmail.com.
You may also use this address to be added to the Drop-seq Google group.

See Releases to download binaries.

See Drop-seq alignment cookbook for detailed usage of these tools.

See Census-seq computational protocols for detailed usage of Census-Seq tools.

See Donor Assignment cookbook for detailed usage of donor assignment and doublet detection tools.

Building from source and installing

Download source: git clone https://github.com/broadinstitute/Drop-seq.git cd Drop-seq

There are two options for building and installing Java code.

  • Build the executable jarfile, a single wrapper script from which all command-line programs can be invoked, installed in the cloned git sandbox.
  • Build a zipfile containing the executable jarfile and wrapper scripts for all command-line programs. The zipfile can be installed in an arbitrary location.

Building the exectable jarfile and single wrapper script

./gradlew installDist

The wrapper script will be dropseq/build/install/dropseq/bin/dropseq. dropseq.bat for Windows.

Build zipfile containing executable jarfile and wrapper scripts

./gradlew distZip

Installing

unzip -d <install-location> ./dropseq/build/distributions/dropseq-<version>.zip Note that the name of the zipfile will be based on the tagged version and state of your git sandbox.

The files will be deployed into a subdirectory of <install-location> above, with name based on the name of the zipfile.

Building Drop-seq R libraries

You are encouraged to use the pre-built binaries in Releases, but if you want to build from (possibly unstable) sources, you can build from github source as follows:

For each library in src/R/packages, you can install using devtools::install_github, e.g.

devtools::install_github("broadinstitute/Drop-seq", subdir="/src/R/packages/DropSeq.utilities")

Alternately, you can download sources and use R CMD BUILD and R CMD INSTALL as usual.

Owner

  • Name: Broad Institute
  • Login: broadinstitute
  • Kind: organization
  • Location: Cambridge, MA

Broad Institute of MIT and Harvard

GitHub Events

Total
  • Issues event: 29
  • Watch event: 9
  • Delete event: 46
  • Issue comment event: 57
  • Push event: 145
  • Pull request review comment event: 8
  • Pull request review event: 7
  • Pull request event: 97
  • Fork event: 1
  • Create event: 48
Last Year
  • Issues event: 29
  • Watch event: 9
  • Delete event: 46
  • Issue comment event: 57
  • Push event: 145
  • Pull request review comment event: 8
  • Pull request review event: 7
  • Pull request event: 97
  • Fork event: 1
  • Create event: 48

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 38
  • Total pull requests: 139
  • Average time to close issues: 5 months
  • Average time to close pull requests: 2 days
  • Total issue authors: 23
  • Total pull request authors: 5
  • Average comments per issue: 4.11
  • Average comments per pull request: 0.51
  • Merged pull requests: 123
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 13
  • Pull requests: 58
  • Average time to close issues: 2 months
  • Average time to close pull requests: 1 day
  • Issue authors: 9
  • Pull request authors: 4
  • Average comments per issue: 2.46
  • Average comments per pull request: 0.41
  • Merged pull requests: 46
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jamesnemesh (6)
  • alecw (4)
  • fbrundu (4)
  • wangmhan (3)
  • kshakir (3)
  • Jayesh-Kumar-Sundaram (2)
  • akulan1 (2)
  • drneavin (2)
  • jolespin (2)
  • PJChenCN (1)
  • shishuo16 (1)
  • daliziya (1)
  • gabriella-quinn (1)
  • Azz43 (1)
  • v-mahughes (1)
Pull Request Authors
  • alecw (126)
  • jamesnemesh (51)
  • kshakir (40)
  • mschilli87 (11)
  • jakewendt (2)
  • lbergelson (1)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

dropseq/build.gradle.kts maven
  • com.google.guava:guava 32.1.1-jre implementation
  • org.testng:testng 7.5.1 testImplementation
src/R/packages/DropSeq.utilities/DESCRIPTION cran
  • data.table * imports
src/R/packages/DropSeq.dropulation/DESCRIPTION cran
  • DropSeq.utilities * imports
  • RColorBrewer * imports
  • data.table * imports
  • ggplot2 * imports
  • ggrepel * imports
  • graphics * imports
  • gridExtra * imports
  • purrr * imports
  • scales * imports
  • stats * imports
  • stringr * imports
  • utils * imports
  • vegan * imports
.github/workflows/DropSeq.dropulation.r.yml actions
  • actions/checkout v3 composite
.github/workflows/DropSeq.utilities.r.yml actions
  • actions/checkout v3 composite
.github/workflows/gradle.yml actions
  • actions/checkout v4 composite
  • actions/setup-java v4 composite
  • gradle/actions/dependency-submission 417ae3ccd767c252f5661f1ace9f835f9654f2b5 composite
  • gradle/actions/setup-gradle 417ae3ccd767c252f5661f1ace9f835f9654f2b5 composite
.github/workflows/DropSeq.eqtl.r.yml actions
.github/workflows/R-package.yml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
src/R/packages/DropSeq.eqtl/DESCRIPTION cran
  • GenomicRanges * imports
  • IRanges * imports
  • LDlinkR * imports
  • MASS * imports
  • Matrix * imports
  • MatrixEQTL * imports
  • RACER * imports
  • RColorBrewer * imports
  • Rsamtools * imports
  • Seurat * imports
  • SeuratDisk * imports
  • VennDiagram * imports
  • areaplot * imports
  • beeswarm * imports
  • caret * imports
  • cowplot * imports
  • data.table * imports
  • fitdistrplus * imports
  • futile.logger * imports
  • genetics * imports
  • ggbeeswarm * imports
  • ggplot2 * imports
  • graphics * imports
  • heatmap3 * imports
  • lme4 * imports
  • logger * imports
  • matrixTests * imports
  • muHVT * imports
  • permuco * imports
  • plotrix * imports
  • png * imports
  • purrr * imports
  • qqman * imports
  • qvalue * imports
  • readr * imports
  • stats * imports
  • stringr * imports
  • tictoc * imports
  • utils * imports
  • vegan * imports
  • viridis * imports
  • yaml * imports
  • DropSeq.utilities * suggests
.github/workflows/docker-drop-seq_java.yaml actions
.github/workflows/docker-drop-seq_python.yaml actions
.github/workflows/docker-drop-seq_r.yaml actions
.github/workflows/docker-drop-seq_reusable.yaml actions
  • actions/checkout v4 composite
  • docker/build-push-action v5 composite
  • docker/login-action v3.0.0 composite
  • docker/metadata-action v5 composite
  • docker/setup-buildx-action v3 composite
.github/workflows/python-dropseq.yml actions
  • actions/checkout v4 composite
  • actions/setup-python v3 composite
src/docker/R/Dockerfile docker
  • common latest build
  • ubuntu 24.04 build
src/docker/java/Dockerfile docker
  • common latest build
  • ubuntu 24.04 build
src/docker/python/Dockerfile docker
  • common latest build
  • ubuntu 24.04 build
src/python/pyproject.toml pypi
  • anndata *
  • google-auth *
  • google-cloud-storage *
  • numpy *
  • pandas *
  • pyarrow *
  • python-dateutil *
  • pyyaml *
  • requests *
  • scanpy >=1.11.2
  • scipy *
  • tables *
  • urllib3 *