Martin Morgan

Martin Morgan

5 packages on CRAN

1 packages on GitHub

23 packages on Bioconductor

AffyCompatible

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This package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx annotation files. The package also provides access to GeneChip Operating System (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation files.

AnnotationHub

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This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.

bvbiome

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This package defines a class for representing microbial communities, and offers facilities for common community analysis tasks related to the microbiome.

DirichletMultinomial

bioconductor
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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 This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed further in the man page for this package, ?DirichletMultinomial.

RWebServices

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This package provides mechanisms for automatic function prototyping and exposure of R functionality in a web services environment.

SJava

bioconductor
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An interface from R to Java to create and call Java objects and methods.

Streamer

bioconductor
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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.

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A convenient tool to install and update Bioconductor packages.

data.table

cran
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Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.

affxparser

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Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure.

AnnotationHubData

bioconductor
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These recipes convert a wide variety and a growing number of public bioinformatic data sets into easily-used standard Bioconductor data structures.

BiocParallel

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

BiocStyle

bioconductor
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Provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality.

convert

bioconductor
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Define coerce methods for microarray data objects.

GenomeInfoDb

bioconductor
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Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.

GenomicAlignments

bioconductor
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Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.

GenomicFiles

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This package provides infrastructure for parallel computations distributed 'by file' or 'by range'. User defined MAPPER and REDUCER functions provide added flexibility for data combination and manipulation.

GSEABase

bioconductor
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This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).

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Programmatically access the NIH / NCI Genomic Data Commons RESTful service.

remotes

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Download and install R packages stored in 'GitHub', 'BitBucket', or plain 'subversion' or 'git' repositories. This package provides the 'install_*' functions in 'devtools'. Indeed most of the code was copied over from 'devtools'.

RInno

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Installs shiny apps packaged as stand-alone Electron apps using Inno Setup, an open source software that builds installers for Windows programs <http://www.jrsoftware.org/ishelp/>.

OrganismDbi

bioconductor
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The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.

Rhtslib

bioconductor
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This package provides version 1.1 of the 'HTSlib' C library for high-throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib. Motivation and instructions for use of this package are in the vignette, vignette(package="Rhtslib", "Rhtslib").

Rsamtools

bioconductor
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This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities (see 'LICENCE') for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.

ShortRead

bioconductor
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This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.

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Download and explore datasets from UCSC Xena data hubs, which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded.

SummarizedExperiment

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The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.

VariantAnnotation

bioconductor
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Annotate variants, compute amino acid coding changes, predict coding outcomes.

zlibbioc

bioconductor
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This package uses the source code of zlib-1.2.5 to create libraries for systems that do not have these available via other means (most Linux and Mac users should have system-level access to zlib, and no direct need for this package). See the vignette for instructions on use.