BiocParallel - Bioconductor facilities for parallel evaluation

This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.

Last updated 24 days ago

infrastructurebioconductor-packagecore-package

16.13 score 67 stars 1.1k packages 6.4k scripts 86k downloads

DirichletMultinomial - Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data

Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed further in the man page for this package, ?DirichletMultinomial.

Last updated 24 days ago

immunooncologymicrobiomesequencingclusteringclassificationmetagenomics

10.93 score 11 stars 25 packages 119 scripts 9.2k downloads

rjsoncons - Query, Pivot, Patch, and Validate 'JSON' and 'NDJSON'

Functions to query (filter or transform), pivot (convert from array-of-objects to object-of-arrays, for easy import as 'R' data frame), search, patch (edit), and validate (against 'JSON Schema') 'JSON' and 'NDJSON' strings, files, or URLs. Query and pivot support 'JSONpointer', 'JSONpath' or 'JMESpath' expressions. The implementation uses the 'jsoncons' <https://danielaparker.github.io/jsoncons/> header-only library; the library is easily linked to other packages for direct access to 'C++' functionality not implemented here.

Last updated 2 months ago

7.47 score 9 stars 9 packages 8 scripts 1.0k downloads

cellxgenedp - Discover and Access Single Cell Data Sets in the CELLxGENE Data Portal

The cellxgene data portal (https://cellxgene.cziscience.com/) provides a graphical user interface to collections of single-cell sequence data processed in standard ways to 'count matrix' summaries. The cellxgenedp package provides an alternative, R-based inteface, allowind data discovery, viewing, and downloading.

Last updated 24 days ago

singlecelldataimportthirdpartyclient

6.87 score 8 stars 31 scripts 212 downloads

AlphaMissenseR - Accessing AlphaMissense Data Resources in R

The AlphaMissense publication <https://www.science.org/doi/epdf/10.1126/science.adg7492> outlines how a variant of AlphaFold / DeepMind was used to predict missense variant pathogenicity. Supporting data on Zenodo <https://zenodo.org/record/10813168> include, for instance, 71M variants across hg19 and hg38 genome builds. The 'AlphaMissenseR' package allows ready access to the data, downloading individual files to DuckDB databases for exploration and integration into *R* and *Bioconductor* workflows.

Last updated 24 days ago

snpannotationfunctionalgenomicsstructuralpredictiontranscriptomicsvariantannotationgenepredictionimmunooncology

6.86 score 6 stars 9 scripts 132 downloads

Organism.dplyr - dplyr-based Access to Bioconductor Annotation Resources

This package provides an alternative interface to Bioconductor 'annotation' resources, in particular the gene identifier mapping functionality of the 'org' packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the 'TxDb' packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).

Last updated 24 days ago

annotationsequencinggenomeannotationbioconductor-packagecore-package

6.75 score 3 stars 1 packages 60 scripts 739 downloads

hca - Exploring the Human Cell Atlas Data Coordinating Platform

This package provides users with the ability to query the Human Cell Atlas data repository for single-cell experiment data. The `projects()`, `files()`, `samples()` and `bundles()` functions retrieve summary information on each of these indexes; corresponding `*_details()` are available for individual entries of each index. File-based resources can be downloaded using `files_download()`. Advanced use of the package allows the user to page through large result sets, and to flexibly query the 'list-of-lists' structure representing query responses.

Last updated 24 days ago

softwaresinglecell

4.63 score 53 scripts 139 downloads

RedisParam - Provide a 'redis' back-end for BiocParallel

This package provides a Redis-based back-end for BiocParallel, enabling an alternative mechanism for distributed computation. The The 'manager' distributes tasks to a 'worker' pool through a central Redis server, rather than directly to workers as with other BiocParallel implementations. This means that the worker pool can change dynamically during job evaluation. All features of BiocParallel are supported, including reproducible random number streams, logging to the manager, and alternative 'load balancing' task distributions.

Last updated 24 days ago

infrastructure

4.53 score 17 scripts 128 downloads

Streamer - Enabling stream processing of large files

Large data files can be difficult to work with in R, where data generally resides in memory. This package encourages a style of programming where data is 'streamed' from disk into R via a `producer' and through a series of `consumers' that, typically reduce the original data to a manageable size. The package provides useful Producer and Consumer stream components for operations such as data input, sampling, indexing, and transformation; see package?Streamer for details.

Last updated 24 days ago

infrastructuredataimport

3.30 score 2 scripts 252 downloads