Tag: BSgenome

Bioconductor – RiboCrypt

DOI: 10.18129/B9.bioc.RiboCrypt     Interactive visualization in genomics Bioconductor version: Release (3.14) R Package for interactive visualization and browsing NGS data. It contains a browser for both transcript and genomic coordinate view. In addition a QC and general metaplots are included, among others differential translation plots and gene expression plots….

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Bioconductor – monaLisa

DOI: 10.18129/B9.bioc.monaLisa     Binned Motif Enrichment Analysis and Visualization Bioconductor version: Release (3.14) Useful functions to work with sequence motifs in the analysis of genomics data. These include methods to annotate genomic regions or sequences with predicted motif hits and to identify motifs that drive observed changes in accessibility…

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Bioconductor – BSgenome.Hsapiens.NCBI.GRCh38

DOI: 10.18129/B9.bioc.BSgenome.Hsapiens.NCBI.GRCh38     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see BSgenome.Hsapiens.NCBI.GRCh38. Full genome sequences for Homo sapiens (GRCh38) Bioconductor version: 3.11 Full genome sequences for Homo sapiens (Human) as provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects. Author: The…

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Bioconductor – ProteoDisco

DOI: 10.18129/B9.bioc.ProteoDisco     Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences Bioconductor version: Release (3.14) ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (mutant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript…

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Bioconductor – BSgenome.Mmulatta.UCSC.rheMac10

DOI: 10.18129/B9.bioc.BSgenome.Mmulatta.UCSC.rheMac10     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see BSgenome.Mmulatta.UCSC.rheMac10. Full genome sequences for Macaca mulatta (UCSC version rheMac10) Bioconductor version: 3.11 Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac10, Feb. 2019) and stored in Biostrings…

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Bioconductor – Rariant

    This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see Rariant. Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies Bioconductor version: 3.0 The ‘Rariant’ package identifies single nucleotide variants from sequencing data based on the difference of…

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Bioconductor – BSgenome.Hsapiens.UCSC.hg19

    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see BSgenome.Hsapiens.UCSC.hg19. Full genome sequences for Homo sapiens (UCSC version hg19) Bioconductor version: 3.2 Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. Author:…

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Forge a BSgenome data package

My supervisor has requested that I create coverage plots to visualize BAM alignments of RNA-Seq data. I though a good way to do this would be to use Gviz. We work on the model legume Medicago truncatula which does not have a BSgenome package so I though I’d try and…

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Loading a genome in BSgenome

Loading a genome in BSgenome 1 Is it possible to load a genome assembled by me (sequence not submitted to any database yet) in the BSgenome package for further study? How? BSgenome Bioconductor genome assembly • 1.1k views Same question here. Please, let us know if you figure out how…

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Bioconductor – VanillaICE

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see VanillaICE. A Hidden Markov Model for high throughput genotyping arrays Bioconductor version: 3.4 Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays. Author: Robert Scharpf <rscharpf at jhu.edu>, Kevin Scharpf,…

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Bioconductor – ChIPComp

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see ChIPComp. Quantitative comparison of multiple ChIP-seq datasets Bioconductor version: 3.4 ChIPComp detects differentially bound sharp binding sites across multiple conditions considering matching control. Author: Hao Wu, Li Chen, Zhaohui S.Qin, Chi Wang Maintainer:…

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Bioconductor – chipseq

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see chipseq. chipseq: A package for analyzing chipseq data Bioconductor version: 3.4 Tools for helping process short read data for chipseq experiments Author: Deepayan Sarkar, Robert Gentleman, Michael Lawrence, Zizhen Yao Maintainer: Bioconductor Package…

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Bioconductor – BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major

DOI: 10.18129/B9.bioc.BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major     Full genome sequences for Homo sapiens (UCSC version hg38, based on GRCh38.p12) with injected major alleles (dbSNP151) Bioconductor version: Release (3.13) Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, based on GRCh38.p12) with major allele injected from dbSNP151, and stored in Biostrings…

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BSgenomes for HIV viruses

BSgenomes for HIV viruses 0 Dear Biostars users, I wonder if there are BSgenomes available for HIV viruses? I am trying to identify clusters from CLIP-seq data mapping to the HIV genome with wavClusteR. I stuck at one step as below: `require(BSgenome.Hsapiens.UCSC.hg19) wavclusters <- filterClusters( clusters = clusters, highConfSub =…

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