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GenomicFeatures specifications

Information


Unique identifier OMICS_19627
Name GenomicFeatures
Alternative name GenomicAlignments
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.32.2
Stability Stable
Requirements
methods, stats, Rsamtools, utils, BiocStyle, tools, BSgenome, RUnit, knitr, org.Hs.eg.db, DBI, org.Mm.eg.db, Biostrings(>=2.47.6), BiocGenerics(>=0.1.0), ensembldb, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, RCurl, TxDb.Mmusculus.UCSC.mm10.knownGene, BSgenome.Celegans.UCSC.ce2, Biobase(>=2.15.1), BSgenome.Dmelanogaster.UCSC.dm3(>=1.3.17), XVector(>=0.19.7), rtracklayer(>=1.39.7), biomaRt(>=2.17.1), AnnotationDbi(>=1.41.4), S4Vectors(>=0.17.29), IRanges(>=2.13.23), GenomeInfoDb(>=1.15.4), GenomicRanges(>=1.31.17), RSQLite(>=2.0), RMariaDB, BSgenome.Hsapiens.UCSC.hg19(>=1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Dmelanogaster.UCSC.dm3.ensGene(>=2.7.1), TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, SNPlocs.Hsapiens.dbSNP144.GRCh38, pasillaBamSubset(>=0.0.5), GenomicAlignments(>=1.15.7)
Maintained Yes

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Maintainer


  • person_outline Michael Lawrence

Publication for GenomicFeatures

GenomicFeatures citations

 (63)
call_split

Genome and transcriptome of the natural isopropanol producer Clostridium beijerinckii DSM6423

2018
BMC Genomics
PMCID: 5894183
PMID: 29636009
DOI: 10.1186/s12864-018-4636-7
call_split See protocol

[…] are then used to extract reliable alignments from SAM formatted files. The number of reads matching each genomic object harbored by the reference genome is subsequently computed with the Bioconductor GenomicFeatures package []. If reads matching several genomic objects, the count number is weighted in order to keep the same total number of reads. Finally, the Bioconductor-DESeq package [] with def […]

library_books

Using regulatory genomics data to interpret the function of disease variants and prioritise genes from expression studies

2018
F1000Res
PMCID: 5850119
PMID: 29568492
DOI: 10.5256/f1000research.14748.r30355

[…] ired packages and dependencies from Bioconductor and CRAN: source("https://bioconductor.org/biocLite.R") # uncomment the following line to install packages #biocLite(c("clusterProfiler", "DESeq2", "GenomicFeatures", "GenomicInteractions", "GenomicRanges", "ggplot2", "Gviz", "gwascat", "InteractionSet", "recount", "pheatmap", "RColorBrewer", "rtracklayer", "R.utils", "splitstackshape", "Varian […]

call_split

PREP1 tumor suppressor protects the late replicating DNA by controlling its replication timing and symmetry

2018
Sci Rep
PMCID: 5816642
PMID: 29453404
DOI: 10.1038/s41598-018-21363-4
call_split See protocol

[…] e sequencing was performed using Ion-Torrent Ion Proton P1 system. After eliminating artifacts with FASTX-Toolkit v.0.0.13.2, reads were aligned to the hg19 reference genome using Tophat v2.0.9. Then GenomicFeatures, Genomic Ranges and GenomicAligments R libraries were used to count the number of reads with respect to the annotation reference. Differentially expressed genes in siLuc v. siPREP1 tre […]

library_books

msgbsR: An R package for analysing methylation sensitive restriction enzyme sequencing data

2018
Sci Rep
PMCID: 5794748
PMID: 29391490
DOI: 10.1038/s41598-018-19655-w

[…] AMtools. The rawCounts function takes a list of sorted and indexed BAM files and imports the raw read counts into the R environment. The rawCounts function internally takes advantage of Rsamtools and GenomicFeatures. After alignment, the beginning of each mapped read starts within the cut site of the recognition sequence of the RE. Rsamtools is used to extract the genomic location of the start of […]

library_books

Activity Dependent Regulation of Alternative Cleavage and Polyadenylation During Hippocampal Long Term Potentiation

2017
Sci Rep
PMCID: 5727029
PMID: 29234016
DOI: 10.1038/s41598-017-17407-w

[…] inimum depth of ~75 M reads per sample. Transcriptome alignment was performed using STAR v. 2.4.1c with default settings, and GRCm38/mm10 (Data statistics, Table ). Raw counts were quantified using R GenomicFeatures and GenomicAlignments and RSamtools packages. Differential expression analysis was performed for each time-point separately in DESeq. We excluded outlier samples, as determined by samp […]

library_books

Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR

2017
F1000Res
PMCID: 5747346
PMID: 29333247
DOI: 10.5256/f1000research.14317.r28483

[…] ckages: [1] stats4 parallel stats graphics grDevices utils datasets methods [9] base other attached packages: [1] org.Mm.eg.db_3.4.2 [2] TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 [3] GenomicFeatures_1.30.0 [4] AnnotationDbi_1.40.0 [5] Biobase_2.38.0 [6] GenomicRanges_1.30.0 [7] GenomeInfoDb_1.14.0 [8] IRanges_2.12.0 [9] S4Vectors_0.16.0 [10] BiocGenerics_0.24.0 [11] edgeR_3. […]

Citations

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GenomicFeatures institution(s)
Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA, USA; European Molecular Biology Laboratory Genome Biology Unit, Heidelberg, Germany; The European Bioinformatics Institute, Cambridge, UK; Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
GenomicFeatures funding source(s)
Supported by the National Institutes of Health, National Human Genome Research Group through grants P41 HG004059 and U41 HG004059 and by National Heart, Lung and Blood Institute grants R01 HL086601, R01 HL093076 and R01 HL094635.

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