combinat - combinatorics utilities

routines for combinatorics

Last updated 12 years ago

7.92 score 224 packages 840 scripts 37k downloads

MLInterfaces - Uniform interfaces to R machine learning procedures for data in Bioconductor containers

This package provides uniform interfaces to machine learning code for data in R and Bioconductor containers.

Last updated 24 days ago

classificationclustering

7.62 score 6 packages 78 scripts 878 downloads

ontoProc - processing of ontologies of anatomy, cell lines, and so on

Support harvesting of diverse bioinformatic ontologies, making particular use of the ontologyIndex package on CRAN. We provide snapshots of key ontologies for terms about cells, cell lines, chemical compounds, and anatomy, to help analyze genome-scale experiments, particularly cell x compound screens. Another purpose is to strengthen development of compelling use cases for richer interfaces to emerging ontologies.

Last updated 1 days ago

infrastructuregobioinformaticsgenomicsontology

7.31 score 3 stars 2 packages 71 scripts 470 downloads

ROC - utilities for ROC, with microarray focus

Provide utilities for ROC, with microarray focus.

Last updated 24 days ago

differentialexpression

7.07 score 10 packages 70 scripts 1.9k downloads

gwascat - representing and modeling data in the EMBL-EBI GWAS catalog

Represent and model data in the EMBL-EBI GWAS catalog.

Last updated 24 days ago

genetics

6.07 score 2 packages 108 scripts 1.1k downloads

BiocHail - basilisk and hail

Use hail via basilisk when appropriate, or via reticulate. This package can be used in terra.bio to interact with UK Biobank resources processed by hail.is.

Last updated 2 days ago

infrastructurebioconductorgeneticshail

6.01 score 6 stars 19 scripts 85 downloads

BiocFHIR - Illustration of FHIR ingestion and transformation using R

FHIR R4 bundles in JSON format are derived from https://synthea.mitre.org/downloads. Transformation inspired by a kaggle notebook published by Dr Alexander Scarlat, https://www.kaggle.com/code/drscarlat/fhir-starter-parse-healthcare-bundles-into-tables. This is a very limited illustration of some basic parsing and reorganization processes. Additional tooling will be required to move beyond the Synthea data illustrations.

Last updated 24 days ago

infrastructuredataimportdatarepresentationfhir

5.95 score 4 stars 15 scripts 122 downloads

scviR - experimental inferface from R to scvi-tools

This package defines interfaces from R to scvi-tools. A vignette works through the totalVI tutorial for analyzing CITE-seq data. Another vignette compares outputs of Chapter 12 of the OSCA book with analogous outputs based on totalVI quantifications. Future work will address other components of scvi-tools, with a focus on building understanding of probabilistic methods based on variational autoencoders.

Last updated 24 days ago

infrastructuresinglecelldataimportbioconductorcite-seqscverse

5.69 score 6 stars 11 scripts 124 downloads

TFutils - TFutils

This package helps users to work with TF metadata from various sources. Significant catalogs of TFs and classifications thereof are made available. Tools for working with motif scans are also provided.

Last updated 9 days ago

transcriptomics

4.76 score 19 scripts 236 downloads

parody - Parametric And Resistant Outlier DYtection

Provide routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics.

Last updated 24 days ago

multiplecomparison

4.73 score 1 packages 12 scripts 380 downloads

xenLite - Simple classes and methods for managing Xenium datasets

Define a relatively light class for managing Xenium data using Bioconductor. Address use of parquet for coordinates, SpatialExperiment for assay and sample data. Address serialization and use of cloud storage.

Last updated 24 days ago

infrastructure

4.48 score 1 stars 4 scripts

BiocSklearn - interface to python sklearn via Rstudio reticulate

This package provides interfaces to selected sklearn elements, and demonstrates fault tolerant use of python modules requiring extensive iteration.

Last updated 24 days ago

statisticalmethoddimensionreductioninfrastructure

4.44 score 11 scripts 222 downloads

AnVILBilling - Provide functions to retrieve and report on usage expenses in NHGRI AnVIL (anvilproject.org).

AnVILBilling helps monitor AnVIL-related costs in R, using queries to a BigQuery table to which costs are exported daily. Functions are defined to help categorize tasks and associated expenditures, and to visualize and explore expense profiles over time. This package will be expanded to help users estimate costs for specific task sets.

Last updated 24 days ago

infrastructuresoftware

4.30 score 5 scripts 140 downloads

ivygapSE - A SummarizedExperiment for Ivy-GAP data

Define a SummarizedExperiment and exploratory app for Ivy-GAP glioblastoma image, expression, and clinical data.

Last updated 24 days ago

transcriptionsoftwarevisualizationsurvivalgeneexpressionsequencing

4.20 score 16 scripts 190 downloads

pogos - PharmacOGenomics Ontology Support

Provide simple utilities for querying bhklab PharmacoDB, modeling API outputs, and integrating to cell and compound ontologies.

Last updated 24 days ago

pharmacogenomicspooledscreensimmunooncology

4.18 score 8 scripts 194 downloads

tenXplore - ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics

Perform ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics.

Last updated 24 days ago

immunooncologydimensionreductionprincipalcomponenttranscriptomicssinglecell

4.18 score 7 scripts 140 downloads

hmdbQuery - utilities for exploration of human metabolome database

Define utilities for exploration of human metabolome database, including functions to retrieve specific metabolite entries and data snapshots with pairwise associations (metabolite-gene,-protein,-disease).

Last updated 24 days ago

metabolomicsinfrastructure

4.11 score 13 scripts 216 downloads

Rcollectl - Help use collectl with R in Linux, to measure resource consumption in R processes

Provide functions to obtain instrumentation data on processes in a unix environment. Parse output of a collectl run. Vizualize aspects of system usage over time, with annotation.

Last updated 24 days ago

softwareinfrastructure

3.95 score 3 stars 7 scripts 70 downloads

rhdf5client - Access HDF5 content from HDF Scalable Data Service

This package provides functionality for reading data from HDF Scalable Data Service from within R. The HSDSArray function bridges from HSDS to the user via the DelayedArray interface. Bioconductor manages an open HSDS instance graciously provided by John Readey of the HDF Group.

Last updated 24 days ago

dataimportsoftwareinfrastructure

3.82 score 2 packages 37 scripts 286 downloads

affyContam - structured corruption of affymetrix cel file data

structured corruption of cel file data to demonstrate QA effectiveness

Last updated 24 days ago

infrastructure

3.78 score 1 packages 1 scripts 435 downloads

ssrch - a simple search engine

Demonstrate tokenization and a search gadget for collections of CSV files.

Last updated 24 days ago

infrastructure

3.60 score 20 scripts 114 downloads

pathRender - Render molecular pathways

build graphs from pathway databases, render them by Rgraphviz.

Last updated 24 days ago

graphandnetworkpathwaysvisualization

3.60 score 2 scripts 317 downloads

keggorthology - graph support for KO, KEGG Orthology

graphical representation of the Feb 2010 KEGG Orthology. The KEGG orthology is a set of pathway IDs that are not to be confused with the KEGG ortholog IDs.

Last updated 24 days ago

pathwaysgraphandnetworkvisualizationkegg

3.48 score 8 scripts 466 downloads

arrayMvout - multivariate outlier detection for expression array QA

This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate

Last updated 24 days ago

infrastructuremicroarrayqualitycontrol

3.34 score 11 scripts 386 downloads

ldblock - data structures for linkage disequilibrium measures in populations

Define data structures for linkage disequilibrium measures in populations.

Last updated 24 days ago

3.30 score 10 scripts 352 downloads

parglms - support for parallelized estimation of GLMs/GEEs

This package provides support for parallelized estimation of GLMs/GEEs, catering for dispersed data.

Last updated 24 days ago

3.30 score 3 scripts 220 downloads

vtpnet - variant-transcription factor-phenotype networks

variant-transcription factor-phenotype networks, inspired by Maurano et al., Science (2012), PMID 22955828

Last updated 24 days ago

network

3.30 score 1 scripts 240 downloads

RbcBook1 - Support for Springer monograph on Bioconductor

tools for building book

Last updated 24 days ago

software

3.30 score 1 scripts 298 downloads