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 20 days ago

infrastructurebioconductor-packagecore-packageu24ca289073cpp

17.40 score 67 stars 1.1k dependents 7.3k scripts 79k 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 This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed further in the man page for this package, ?DirichletMultinomial.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 4 months ago

immunooncologymicrobiomesequencingclusteringclassificationmetagenomicsgsl

10.97 score 11 stars 26 dependents 125 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 6 months ago

cpp

7.08 score 9 stars 9 dependents 8 scripts 859 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 4 months ago

snpannotationfunctionalgenomicsstructuralpredictiontranscriptomicsvariantannotationgenepredictionimmunooncology

6.86 score 8 stars 10 scripts 149 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 4 months ago

annotationsequencinggenomeannotationbioconductor-packagecore-package

6.77 score 3 stars 1 dependents 63 scripts 767 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 4 months ago

singlecelldataimportthirdpartyclient

6.64 score 8 stars 27 scripts 208 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 4 months ago

infrastructure

4.53 score 17 scripts 162 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 4 months ago

softwaresinglecell

3.34 score 55 scripts 242 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 4 months ago

infrastructuredataimport

3.30 score 2 scripts 282 downloads