Showing 12 of total 12 results (show query)
reside-ic
ids:Generate Random Identifiers
Generate random or human readable and pronounceable identifiers.
Maintained by Rich FitzJohn. Last updated 3 years ago.
94 stars 13.27 score 175 scripts 165 dependents
bioc
GenomicDataCommons:NIH / NCI Genomic Data Commons Access
Programmatically access the NIH / NCI Genomic Data Commons RESTful service.
Maintained by Sean Davis. Last updated 2 months ago.
dataimportsequencingapi-clientbioconductorbioinformaticscancercore-servicesdata-sciencegenomicsncitcgavignette
87 stars 11.94 score 238 scripts 12 dependents
crunch-io
crunch:Crunch.io Data Tools
The Crunch.io service <https://crunch.io/> provides a cloud-based data store and analytic engine, as well as an intuitive web interface. Using this package, analysts can interact with and manipulate Crunch datasets from within R. Importantly, this allows technical researchers to collaborate naturally with team members, managers, and clients who prefer a point-and-click interface.
Maintained by Greg Freedman Ellis. Last updated 8 days ago.
9 stars 10.47 score 200 scripts 2 dependents
mlr-org
mlr3misc:Helper Functions for 'mlr3'
Frequently used helper functions and assertions used in 'mlr3' and its companion packages. Comes with helper functions for functional programming, for printing, to work with 'data.table', as well as some generally useful 'R6' classes. This package also supersedes the package 'BBmisc'.
Maintained by Marc Becker. Last updated 4 months ago.
machine-learningmiscellaneousmlr3
12 stars 10.28 score 302 scripts 42 dependentsbioc
GSEABase:Gene set enrichment data structures and methods
This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).
Maintained by Bioconductor Package Maintainer. Last updated 2 months ago.
geneexpressiongenesetenrichmentgraphandnetworkgokegg
10.27 score 1.5k scripts 77 dependents
grunwaldlab
metacoder:Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data
Reads, plots, and manipulates large taxonomic data sets, like those generated from modern high-throughput sequencing, such as metabarcoding (i.e. amplification metagenomics, 16S metagenomics, etc). It provides a tree-based visualization called "heat trees" used to depict statistics for every taxon in a taxonomy using color and size. It also provides various functions to do common tasks in microbiome bioinformatics on data in the 'taxmap' format defined by the 'taxa' package. The 'metacoder' package is described in the publication by Foster et al. (2017) <doi:10.1371/journal.pcbi.1005404>.
Maintained by Zachary Foster. Last updated 2 months ago.
community-diversityhierarchicalmetabarcodingpcrtaxonomytreescpp
140 stars 9.64 score 328 scriptsbioc
cmapR:CMap Tools in R
The Connectivity Map (CMap) is a massive resource of perturbational gene expression profiles built by researchers at the Broad Institute and funded by the NIH Library of Integrated Network-Based Cellular Signatures (LINCS) program. Please visit https://clue.io for more information. The cmapR package implements methods to parse, manipulate, and write common CMap data objects, such as annotated matrices and collections of gene sets.
Maintained by Ted Natoli. Last updated 5 months ago.
dataimportdatarepresentationgeneexpressionbioconductorbioinformaticscmap
90 stars 8.86 score 298 scripts
philips-software
latrend:A Framework for Clustering Longitudinal Data
A framework for clustering longitudinal datasets in a standardized way. The package provides an interface to existing R packages for clustering longitudinal univariate trajectories, facilitating reproducible and transparent analyses. Additionally, standard tools are provided to support cluster analyses, including repeated estimation, model validation, and model assessment. The interface enables users to compare results between methods, and to implement and evaluate new methods with ease. The 'akmedoids' package is available from <https://github.com/MAnalytics/akmedoids>.
Maintained by Niek Den Teuling. Last updated 3 months ago.
cluster-analysisclustering-evaluationclustering-methodsdata-sciencelongitudinal-clusteringlongitudinal-datamixture-modelstime-series-analysis
30 stars 6.77 score 26 scripts
pierreroudier
spectacles:Storing, Manipulating and Analysis Spectroscopy and Associated Data
Stores and eases the manipulation of spectra and associated data, with dedicated classes for spatial and soil-related data.
Maintained by Pierre Roudier. Last updated 2 years ago.
11 stars 6.17 score 45 scripts 1 dependents
ucd-serg
serocalculator:Estimating Infection Rates from Serological Data
Translates antibody levels measured in cross-sectional population samples into estimates of the frequency with which seroconversions (infections) occur in the sampled populations. Replaces the previous `seroincidence` package.
Maintained by Kristina Lai. Last updated 5 days ago.
epidemiologyincidence-estimationseroepidemiology
6 stars 5.61 score 13 scripts
lawremi
rsolr:R to Solr Interface
A comprehensive R API for querying Apache Solr databases. A Solr core is represented as a data frame or list that supports Solr-side filtering, sorting, transformation and aggregation, all through the familiar base R API. Queries are processed lazily, i.e., a query is only sent to the database when the data are required.
Maintained by Michael Lawrence. Last updated 3 years ago.
9 stars 3.65 score 6 scripts