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

rgcca-factory/RGCCA
  • * DESCRIPTION

Size: 27.4 MB - Last synced: 11 days ago - Pushed: 11 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

askomics/askoR
  • * DESCRIPTION

Size: 33.9 MB - Last synced: 30 days ago - Pushed: 3 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

charade/swan
  • * DESCRIPTION

Size: 15.7 MB - Last synced: over 1 year 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

pooranis/Maaslin2_bioc
  • * DESCRIPTION

Last synced: over 1 year 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

yuhenglu/tagseq
  • * DESCRIPTION

Size: 16.9 MB - Last synced: over 1 year 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

hivdiversity/motifbinner2
  • * DESCRIPTION

Size: 5.3 MB - Last synced: over 1 year 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

vimc/orderly
  • * DESCRIPTION

Last synced: about 1 year 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

charade/dsib
  • * DESCRIPTION

Size: 10.3 MB - Last synced: over 1 year 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

epifluidlab/cofragr
  • * DESCRIPTION

Size: 150 KB - Last synced: 10 months ago - Pushed: 10 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