Valerie Obenchain

Valerie Obenchain

7 packages on Bioconductor

BiocParallel

bioconductor
99.99th

Percentile

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

ensemblVEP

bioconductor
99.99th

Percentile

Query the Ensembl Variant Effect Predictor via the perl API

GenomicAlignments

bioconductor
99.99th

Percentile

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

bioconductor
99.99th

Percentile

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.

OrganismDbi

bioconductor
99.99th

Percentile

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.

Rsamtools

bioconductor
99.99th

Percentile

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.

SummarizedExperiment

bioconductor
99.99th

Percentile

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.