Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
Package Usage: cran: optparse
Command Line Option Parser
20 versions
Latest release: 4 months ago
10 dependent packages
44,728 downloads last month
View more package details: https://packages.ecosyste.ms/registries/cran.r-project.org/packages/optparse
View more repository details: https://repos.ecosyste.ms/hosts/GitHub/repositories/trevorld%2Fr-optparse
Dependent Repos 163
bbuchsbaum/rMVPA
Multivoxel Pattern Analysis in R- * DESCRIPTION
Size: 84.4 MB - Last synced: 23 days ago - Pushed: 23 days ago
ptelomere/RGalaxy
- * DESCRIPTION
Size: 601 KB - Last synced: 9 months ago - Pushed: about 9 years ago
GeneticAnalysisinBiobanks/GRAB
- * DESCRIPTION
Size: 398 MB - Last synced: 5 months ago - Pushed: 5 months ago
cameronbracken/pgfSweave
Quality graphics and speedy compilation with Sweave- * DESCRIPTION
Size: 8.29 MB - Last synced: about 1 year ago - Pushed: about 11 years ago
TearsWillFall/ULPwgs
Utility tool that integrates commonly used bioinformatic tools for ULP-WGS analysis- * DESCRIPTION
Size: 98.9 MB - Last synced: 1 day ago - Pushed: 2 days ago
Sage-Bionetworks/synapseusagereports
- * DESCRIPTION
Size: 199 KB - Last synced: about 1 month ago - Pushed: over 2 years ago
RHoMIS/rhomis-R-package
An R package for essential processing of data collected with RHoMIS- * DESCRIPTION
Size: 7.38 MB - Last synced: 6 months ago - Pushed: 6 months ago
lima1/sttkit
Pipeline for SpatialTranscriptomics and 10X Visium data- * DESCRIPTION
Size: 541 KB - Last synced: 5 days ago - Pushed: 5 days ago
epiforecasts/covid-rt-estimates
National and subnational estimates of the time-varying reproduction number for Covid-19- * DESCRIPTION
Size: 7.08 GB - Last synced: 7 months ago - Pushed: almost 2 years ago
philliplab/MotifBinner
- * DESCRIPTION
Size: 2.85 MB - Last synced: 9 months ago - Pushed: over 3 years ago
ben-laufer/DMRichR
A R package and executable for the preprocessing, statistical analysis, and downstream testing and visualization of differentially methylated regions (DMRs) from CpG count matrices (Bismark cytosine reports)- * DESCRIPTION
Size: 4.25 MB - Last synced: 8 months ago - Pushed: 8 months ago
eahrne/SafeQuant
A Toolbox for analysis of Proteomics Data- * DESCRIPTION
Size: 498 MB - Last synced: 7 months ago - Pushed: about 3 years ago
WHops/NAHRwhals
R package and wrapper functions for identifying serial structural variations from genome assemblies- * DESCRIPTION
Size: 28.5 MB - Last synced: about 1 month ago - Pushed: about 1 month ago
richfitz/remake
Make-like declarative workflows in R- * DESCRIPTION
Size: 819 KB - Last synced: 3 months ago - Pushed: almost 6 years ago
davidaknowles/leafcutter
Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard- * leafcutter/DESCRIPTION
Size: 42.6 MB - Last synced: 24 days ago - Pushed: 3 months ago
petrelharp/context
Context-dependent mutation rate inference machinery.- * contextutils/DESCRIPTION
Size: 40.9 MB - Last synced: 15 days ago - Pushed: 4 months ago
jrnold/r4ds-exercise-solutions
Exercise solutions to "R for Data Science"- * DESCRIPTION
Size: 110 MB - Last synced: about 1 month ago - Pushed: 3 months ago
Sage-Bionetworks/dccvalidator
Metadata Validation for Data Coordinating Centers- * DESCRIPTION
Size: 9.07 MB - Last synced: about 1 month ago - Pushed: about 1 year ago
biobakery/Maaslin2
MaAsLin2: Microbiome Multivariate Association with Linear Models- * DESCRIPTION
Size: 1.15 MB - Last synced: about 2 months ago - Pushed: about 2 months ago
zellerlab/siamcat
R package for Statistical Inference of Associations between Microbial Communities And host phenoType- * DESCRIPTION
Size: 64.4 MB - Last synced: 4 months ago - Pushed: 4 months ago
mdietze/pecan Fork of PecanProject/pecan
The Predictive Ecosystem Analyzer (PEcAn) is an integrated ecological bioinformatics toolbox.- * base/settings/DESCRIPTION
Size: 389 MB - Last synced: about 1 month ago - Pushed: 2 months ago
UCSF-DSCOLAB/cyclone
- * cyclone/DESCRIPTION
Size: 15.4 MB - Last synced: 6 months ago - Pushed: 6 months ago
lima1/PureCN
Copy number calling and variant classification using targeted short read sequencing- * DESCRIPTION
Size: 18.9 MB - Last synced: 4 days ago - Pushed: 4 days ago
cancerit/RCRISPR
R library for CRISPR analysis- * DESCRIPTION
Size: 16.6 MB - Last synced: 7 months ago - Pushed: about 1 year ago
bergerm1/GenomeDerivedDiagnosis
- * DESCRIPTION
Size: 19.6 MB - Last synced: about 1 year ago - Pushed: over 3 years ago
alexrecuenco/TexExamRandomizer
R package, randomizing LaTeX exams- * DESCRIPTION
Size: 4.47 MB - Last synced: 22 days ago - Pushed: 4 months ago
sarangian/bulkRNASeqPIPE
Differential Expression Analysis of bulk-RNASeq data- * utility/deaRscripts/DESCRIPTION
Size: 347 MB - Last synced: about 1 year ago - Pushed: over 3 years ago
jschmiedel/tempura
R package to fit thermodynamic models to deep mutational scanning data- * DESCRIPTION
Size: 698 KB - Last synced: about 1 year ago - Pushed: over 3 years ago
lianos/GenomicCache
Extensions to Bioconductor GenomicFeatures package. Primarily, this implements a more "Gene Centric" view on the world, as opposed to base GenomicFeature's transcript/exon/cds centric view.- >= 0.9.1 DESCRIPTION
Size: 239 KB - Last synced: about 1 year ago - Pushed: over 5 years ago
resampling-stats/resampling-with
Source repository for third edition of "Resampling: The New Statistics"- * DESCRIPTION
Size: 13.9 MB - Last synced: about 1 month ago - Pushed: 2 months ago
martin3141/fmriqa
An R package for fMRI quality assurance- * DESCRIPTION
Size: 2.14 MB - Last synced: 26 days ago - Pushed: over 4 years ago
llaniewski/rtemplate
R Template tool. Something like Sweave, but with more php-like syntax. Just try it already!- >= 1.2.0 DESCRIPTION
Size: 60.5 KB - Last synced: 4 months ago - Pushed: 4 months ago
jknightlab/mePipe
Functions to support running of Matrix-eQTL analysis pipeline. This includes support for adding principle components as covariates and determining the optimal number of principal components to include.- * DESCRIPTION
Size: 570 KB - Last synced: about 1 year ago - Pushed: over 8 years ago
ibest/grcScripts2
University of Idaho Genomics Resources Core HTS Processing scripts as an R package- * DESCRIPTION
Size: 273 KB - Last synced: about 2 months ago - Pushed: about 9 years ago
maragkakislab/nanoplen
Package for the analysis of the nanopore read lengths, e.g. to calculate the significant differential transcript length.- * DESCRIPTION
Size: 8.1 MB - Last synced: 3 months ago - Pushed: 3 months ago
dhelekal/CaveDive
- * DESCRIPTION
Size: 165 MB - Last synced: about 1 year ago - Pushed: over 1 year ago
dtenenba/RGalaxy2
- * DESCRIPTION
Size: 258 KB - Last synced: about 1 year ago - Pushed: almost 10 years ago
dkainer/RWRtoolkit
a set of command-line and R tools for performing Random-walk with Restart analyses on multiplex networks in any species- * DESCRIPTION
Size: 664 KB - Last synced: about 2 months ago - Pushed: about 2 months ago
seaflow-uw/popcycle
Popcycle is an R package that offers reproducible analytical tools to analyze flow cytometry data collected by SeaFlow- * DESCRIPTION
Size: 49.6 MB - Last synced: about 2 months ago - Pushed: about 2 months ago
sakrejda/uciekaj
Convenience control functions for JAGS through rjags.- * package_dir/DESCRIPTION
Size: 250 KB - Last synced: about 1 year ago - Pushed: over 9 years ago
epifluidlab/cragr
R package for CRAG- * DESCRIPTION
Size: 31.8 MB - Last synced: about 1 month ago - Pushed: 4 months ago
biobakery/melonnpan
Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles- * DESCRIPTION
Size: 3.81 MB - Last synced: about 2 months ago - Pushed: about 2 months ago
HannahVMeyer/PhenotypeSimulator
- * DESCRIPTION
Size: 18.7 MB - Last synced: 14 days ago - Pushed: 3 months ago
dphansti/mango
chia pet analysis software- * DESCRIPTION
Size: 37.1 MB - Last synced: 7 months ago - Pushed: over 5 years ago
PF2-pasteur-fr/SARTools
Statistical Analysis of RNA-Seq Tools- * DESCRIPTION
Size: 2.17 MB - Last synced: 7 months ago - Pushed: 11 months ago
traitecoevo/competition_kernels
:seedling: Emergent shapes of trait-based competition functions from resource-based models :deciduous_tree::evergreen_tree::palm_tree:- * DESCRIPTION
Size: 3.48 MB - Last synced: 4 months ago - Pushed: about 3 years ago
lehner-lab/DiMSum
An error model and pipeline for analyzing deep mutational scanning (DMS) data and diagnosing common experimental pathologies- * DESCRIPTION
Size: 2.93 MB - Last synced: 16 days ago - Pushed: about 1 month ago
VizGrimoire/GrimoireLib
- * vizgrimoire/DESCRIPTION
Size: 34.3 MB - Last synced: about 2 months ago - Pushed: over 7 years ago
phac-nml/wade-old
A flexible and customizable method to extract specific genes from a large number of genomes at once- * DESCRIPTION
Size: 1.25 MB - Last synced: about 1 year ago - Pushed: over 1 year ago
diptavo/GAUSS
Gene-set Association analysis Using Sparse Signals- * GAUSS/DESCRIPTION
Size: 496 MB - Last synced: 7 months ago - Pushed: almost 3 years ago
Sage-Bionetworks/cleanAD
Tools for cleaning and organizing study data for the AD Knowledge Portal.- * DESCRIPTION
Size: 123 KB - Last synced: about 1 month ago - Pushed: 8 months ago
geoffrosen/hmp_mapping
Mapping files between HMP metagenomic data and HMP 16S data- * requirements/Maaslin/DESCRIPTION
Size: 2.3 MB - Last synced: about 1 year ago - Pushed: almost 9 years ago
Sage-Bionetworks/porTools
This package helps maintain content in Sage portals.- * DESCRIPTION
Size: 73.2 KB - Last synced: about 1 month ago - Pushed: almost 2 years ago
leslielab/genomiccache
Keep original code compatible with newer versions of Bioconductor- >= 0.9.1 DESCRIPTION
Size: 10.5 MB - Last synced: over 1 year ago
jhchung/geneARTP
Adaptive rank truncated product analysis using gene based p-values.- * DESCRIPTION
Size: 210 KB - Last synced: about 1 year ago - Pushed: over 8 years ago
esovetkin/ledger-plots
R functions to plot data from your ledger- * ledgerplots/DESCRIPTION
Size: 6.48 MB - Last synced: about 1 year ago - Pushed: about 4 years ago
biobakery/Macarron
- * DESCRIPTION
Size: 2.45 MB - Last synced: about 2 months ago - Pushed: about 2 months ago
homonecloco/bio.tilling
R scripts to plot/analyse coverage from BED files- * DESCRIPTION
Size: 7.97 MB - Last synced: about 1 year ago - Pushed: about 5 years ago
cran/opm
Tools for analysing OmniLog(R) Phenotype Microarray data- * DESCRIPTION
Size: 17 MB - Last synced: 7 months ago - Pushed: about 10 years ago
dtenenba/test2
- * package/DESCRIPTION
Size: 258 KB - Last synced: about 1 year ago - Pushed: about 10 years ago
dtenenba/RGalaxy-vignette-changes
- * DESCRIPTION
Size: 449 KB - Last synced: about 1 year ago - Pushed: over 11 years ago
hiplot/hiplotlib
Infrastructure of Hiplot (ORG)- * DESCRIPTION
Size: 474 KB - Last synced: 4 months ago - Pushed: 4 months ago
paulbuchana/BiocCheck
BioCheck Repo from the Bioconductor Project- * DESCRIPTION
Size: 5.18 MB - Last synced: 11 months ago - Pushed: about 10 years ago
SystemsGenetics/KINC.R
Supplemental R package for KINC- * DESCRIPTION
- * DESCRIPTION
Size: 202 KB - Last synced: 7 months ago - Pushed: over 2 years ago
michaelgruenstaeudl/PACVr
Plastome Assembly Coverage Visualization in R- >= 1.6.0 DESCRIPTION
Size: 49.8 MB - Last synced: 4 days ago - Pushed: about 1 month ago
kharchenkolab/dropEst
Pipeline for initial analysis of droplet-based single-cell RNA-seq data- * dropestr/DESCRIPTION
Size: 47.1 MB - Last synced: 1 minute ago - Pushed: almost 2 years ago
traitecoevo/experimentr
root- * DESCRIPTION
Size: 365 KB - Last synced: 4 months ago - Pushed: over 8 years ago
gtonkinhill/fastbaps
A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data- * DESCRIPTION
Size: 2.27 MB - Last synced: 7 months ago - Pushed: over 1 year ago
astrazeneca-cgr-publications/PEACOK
Phenome Exome Association and Correlation Of Key phenotypes- * PEACOK/DESCRIPTION
Size: 2.23 MB - Last synced: 7 months ago - Pushed: over 2 years ago
cran/pgfSweave
Quality speedy graphics compilation and caching with Sweave- * DESCRIPTION
Size: 3.39 MB - Last synced: 9 months ago - Pushed: about 10 years ago
michelk/logbuch.R
Keep track of you workday-hours in a diary style- * DESCRIPTION
Size: 114 KB - Last synced: about 1 year ago - Pushed: over 6 years ago
pjshort/denovoTF
Calculating change in binding affinity for predicted TF binding sites as a result of de novo mutations in non-coding regions. Uses JASPAR database for TF binding prediction.- * DESCRIPTION
Size: 107 KB - Last synced: about 1 year ago - Pushed: about 6 years ago
parlametria/leggoR
Acesso, tradução e modelos usando dados do congresso nacional- * DESCRIPTION
Size: 45.2 MB - Last synced: about 1 month ago - Pushed: about 2 years ago
parlametria/perfil-parlamentarR
- * DESCRIPTION
Size: 37.4 MB - Last synced: about 1 year ago - Pushed: over 2 years ago
dzhw/variableMetadataPreparation
This tool extracts metadata of variables and creates JSON files for the mdm.- == 1.7.1 DESCRIPTION
Size: 329 MB - Last synced: about 2 months ago - Pushed: over 2 years ago
biobakery/melonnpan
Model-Based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles- * DESCRIPTION
Size: 13.9 MB - Last synced: over 1 year ago
dtenenbaum/RGalaxy.test
post procter luigi loquat hoc- * DESCRIPTION
Size: 242 KB - Last synced: about 1 year ago - Pushed: over 10 years ago
lifs-tools/flipr
Fragment-based Lipid Relative Intensity Prediction- * DESCRIPTION
Size: 13.7 MB - Last synced: about 1 year ago - Pushed: over 2 years ago
jhchung/candidateGeneSetAnalysis
R package to perform candidate gene analysis on high throughput sequencing data.- * DESCRIPTION
Size: 137 KB - Last synced: about 1 year ago - Pushed: almost 9 years ago
Data-Science-Brigade/modelo-epidemiologico-sc
Bayesian epidemiological model, with a focus on the state of Santa Catarina and its micro and macroregions. https://arxiv.org/abs/2104.01133- >= 1.6.6 epiCata/DESCRIPTION
- >= 1.6.6 epiCataPlot/DESCRIPTION
Size: 21.8 MB - Last synced: 4 months ago - Pushed: over 2 years ago
transportenergy/database
Tools for accessing and maintaining the iTEM model & historical databases- * R/item/DESCRIPTION
Size: 4.34 MB - Last synced: about 7 hours ago - Pushed: 21 days ago
genomicsengland/gel-coverage
- * old/coverage-summary/gelCoverageR/DESCRIPTION
Size: 114 MB - Last synced: 23 days ago - Pushed: almost 2 years ago
meyer-lab-cshl/plinkQC
R package for quality control of plink genetic datasets- * DESCRIPTION
Size: 17.2 MB - Last synced: 11 days ago - Pushed: 5 months ago
infotroph/pecan-pr-sandbox
A clone of PecanProject/pecan, used for testing CI changes without annoying the whole team- * base/settings/DESCRIPTION
Size: 388 MB - Last synced: about 1 month ago - Pushed: about 1 month ago
nanu1605/pecan Fork of PecanProject/pecan
The Predictive Ecosystem Analyzer (PEcAn) is an integrated ecological bioinformatics toolbox.- * base/settings/DESCRIPTION
Size: 389 MB - Last synced: about 2 months ago - Pushed: about 2 months ago
r-forge/opm
Read-only mirror of "opm" from r-forge SVN.- * pkg/opm/DESCRIPTION
- * trunk/opm_in/DESCRIPTION
Size: 188 MB - Last synced: 9 months ago - Pushed: almost 2 years ago
r-forge/pgfsweave
Read-only mirror of "pgfsweave" from r-forge SVN.- * pkg/DESCRIPTION
Size: 3.5 MB - Last synced: 9 months ago - Pushed: about 2 years ago
mskilab-org/JaBbA
MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.- * DESCRIPTION
Size: 18 MB - Last synced: about 2 months ago - Pushed: 6 months ago