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combinat - Combinatorics Utilities

Provides routines for combinatorial enumeration including generation of all combinations, permutations, and lattice points on hypercuboids and simplex lattices. Includes utilities for multinomial distributions: the multinomial probability mass function, random sampling with varying parameters, and encoding conversions between simplex representations. Also supplies exact and log-scale factorial computation and the generalized binomial coefficient for real-valued n. Package functions include procedures described in Reingold, Nievergelt and Deo (1977) Combinatorial Algorithms: Theory and Practice (dl.acm.org/citation.cfm?id=1096489), Feller volume 1, and Nijenhuis and Wilf (1978) Combinatorial Algorithms for Computers and Calculators (ISBN 0125192606 / 9780125192606).

Last updated

8.19 score 234 dependents 890 scripts 61k 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.

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classificationclustering

7.97 score 5 dependents 82 scripts 1.7k 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.

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infrastructuregobioinformaticsgenomicsontology

7.74 score 5 stars 2 dependents 102 scripts 656 downloads

ROC - utilities for ROC, with microarray focus

Provide utilities for ROC, with microarray focus.

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differentialexpression

7.26 score 12 dependents 2.8k downloads

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

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

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genetics

6.69 score 2 dependents 151 scripts 1.7k downloads

ontoProc2 - Ontology Facilities Based on INCAtools Semantic SQL

This package provides ontology facilities based on INCAtools Semantic SQL. Tooling is provided to retrieve and cache SQLite databases representing curated ontologies. ontologyIndex ontology_index instances can be produced. Anthropic's Claude was used in the development of S7 classes and methods and in the production of documentation.

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infrastructuredatarepresentationpathwayssinglecell

6.11 score 1 stars 1 dependents 19 scripts 498 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.

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infrastructuredataimportdatarepresentationfhir

6.00 score 4 stars 25 scripts 360 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.

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multiplecomparison

4.78 score 1 dependents 20 scripts 604 downloads

ivygapSE - A SummarizedExperiment for Ivy-GAP data

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

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transcriptionsoftwarevisualizationsurvivalgeneexpressionsequencing

4.52 score 22 scripts 462 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.

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infrastructurebioconductorgeneticshail

4.46 score 6 stars 16 scripts 216 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.

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infrastructuresoftware

4.30 score 7 scripts 314 downloads

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.

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statisticalmethoddimensionreductioninfrastructure

4.18 score 15 scripts 464 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.

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softwareinfrastructure

4.07 score 3 stars 13 scripts 183 downloads

PlinkMatrix - DelayedArray interface for plink bed files

This package provides a DelayedArray interface for plink bed files. There is support for interfacing to plink genotype data via RangedSummarizedExperiment. Example data from the GEUVADIS project (internationalgenome.org) are used for demonstration.

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infrastructuregeneticscpp

4.04 score 1 stars 11 scripts 284 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.

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infrastructureu24ca289073

4.00 score 1 stars 4 scripts 272 downloads

pogos - PharmacOGenomics Ontology Support

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

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pharmacogenomicspooledscreensimmunooncology

4.00 score 10 scripts

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.

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immunooncologydimensionreductionprincipalcomponenttranscriptomicssinglecell

4.00 score 8 scripts 582 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

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infrastructuremicroarrayqualitycontrol

3.89 score 13 scripts 608 downloads

pathRender - Render molecular pathways

build graphs from pathway databases, render them by Rgraphviz.

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graphandnetworkpathwaysvisualization

3.78 score 2 scripts 586 downloads

affyContam - structured corruption of affymetrix cel file data

structured corruption of cel file data to demonstrate QA effectiveness

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infrastructure

3.78 score 1 dependents 5 scripts 578 downloads

ssrch - a simple search engine

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

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infrastructure

3.70 score 25 scripts 343 downloads

harbChIP - Experimental Data Package: harbChIP

data from a yeast ChIP-chip experiment

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experimentdatasaccharomyces_cerevisiae_datasequencingdatadatapkg

3.68 score 24 scripts

leeBamViews - leeBamViews -- multiple yeast RNAseq samples excerpted from Lee 2009

data from PMID 19096707; prototype for managing multiple NGS samples

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experimentdatasaccharomyces_cerevisiae_datasequencingdatarnaseqdatasnpdatadatapkg

3.62 score 21 scripts

golubEsets - exprSets for golub leukemia data

representation of public golub data with some covariate data of provenance unknown to the maintainer at present; now employs ExpressionSet format

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experimentdatagenomecancerdataleukemiacancerdatadatapkg

3.58 score 190 scripts

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.

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transcriptomics

3.45 score 28 scripts 655 downloads

ldblock - data structures for linkage disequilibrium measures in populations

Define data structures for linkage disequilibrium measures in populations.

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3.41 score 13 scripts 582 downloads

parglms - support for parallelized estimation of GLMs/GEEs

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

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3.30 score 4 scripts 516 downloads

vtpnet - variant-transcription factor-phenotype networks

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

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network

3.30 score 6 scripts 514 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.

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pathwaysgraphandnetworkvisualizationkegg

3.30 score 8 scripts

RbcBook1 - Support for Springer monograph on Bioconductor

tools for building book

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software

3.30 score 2 scripts 801 downloads