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11 packages on Bioconductor

AnnotationDbi

bioconductor
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Provides user interface and database connection code for annotation data packages using SQLite data storage.

AnnotationForge

bioconductor
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Provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi.

BSgenome

bioconductor
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Infrastructure shared by all the Biostrings-based genome data packages

ChIPpeakAnno

bioconductor
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The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. Starting 2.0.5, new functions have been added for finding the peaks with bi-directional promoters with summary statistics (peaksNearBDP), for summarizing the occurrence of motifs in peaks (summarizePatternInPeaks) and for adding other IDs to annotated peaks or enrichedGO (addGeneIDs). This package leverages the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat packages.

CRISPRseek

bioconductor
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The package includes functions to find potential guide RNAs for input target sequences, optionally filter guide RNAs without restriction enzyme cut site, or without paired guide RNAs, genome-wide search for off-targets, score, rank, fetch flank sequence and indicate whether the target and off-targets are located in exon region or not. Potential guide RNAs are annotated with total score of the top5 and topN off-targets, detailed topN mismatch sites, restriction enzyme cut sites, and paired guide RNAs. If GeneRfold and GeneR are installed (http://bioconductor.case.edu/bioconductor/2.8/bioc/html/GeneRfold.html, http://bioc.ism.ac.jp/packages/2.8/bioc/html/GeneR.html), then the minimum free energy and bracket notation of secondary structure of gRNA and gRNA backbone constant region will be included in the summary file. This package leverages Biostrings and BSgenome packages.

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.

GenomicTuples

bioconductor
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GenomicTuples defines general purpose containers for storing genomic tuples. It aims to provide functionality for tuples of genomic co-ordinates that are analogous to those available for genomic ranges in the GenomicRanges Bioconductor package.

HDF5Array

bioconductor
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This package implements the HDF5Array class for convenient access and manipulation of HDF5 datasets. In order to reduce memory usage and optimize performance, operations on an HDF5Array object are either delayed or executed using a block processing mechanism. The delaying and block processing mechanisms are independent of the on-disk backend and implemented via the DelayedArray class. They even work on ordinary arrays where they can sometimes improve performance.

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.

SummarizedExperiment

bioconductor
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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.

XVector

bioconductor
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Memory efficient S4 classes for storing sequences "externally" (behind an R external pointer, or on disk).