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bioconductor-bsgenome.celegans.ucsc.ce10
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public |
No Summary
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2024-12-29 |
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bioconductor-snplocs.hsapiens.dbsnp144.grch37
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public |
SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped to reference genome GRCh37.p13. WARNING: Note that the GRCh37.p13 genome is a patched version of GRCh37. However the patch doesn't alter chromosomes 1-22, X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for the mitochondrion chromosome. Therefore, the SNPs in this package can be "injected" in BSgenome.Hsapiens.UCSC.hg19 and they will land at the correct position but this injection will exclude chrM (i.e. nothing will be injected in that sequence).
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2024-12-29 |
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bioconductor-snplocs.hsapiens.dbsnp144.grch38
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public |
SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 30, 2015, and contain SNPs mapped to reference genome GRCh38.p2 (a patched version of GRCh38 that doesn't alter chromosomes 1-22, X, Y, MT). Note that these SNPs can be "injected" in BSgenome.Hsapiens.NCBI.GRCh38 or in BSgenome.Hsapiens.UCSC.hg38.
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2024-12-29 |
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bioconductor-mmdiff2
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public |
Statistical Testing for ChIP-Seq data sets
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2024-12-29 |
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bioconductor-bsgenome.cfamiliaris.ucsc.canfam2
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public |
Full genome sequences for Canis lupus familiaris (Dog) as provided by UCSC (canFam2, May 2005) and stored in Biostrings objects.
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2024-12-29 |
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bioconductor-leebamviews
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public |
leeBamViews -- multiple yeast RNAseq samples excerpted from Lee 2009
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2024-12-29 |
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bioconductor-bsgenome.sscrofa.ucsc.susscr3
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public |
Full genome sequences for Sus scrofa (Pig) as provided by UCSC (susScr3, Aug. 2011) and stored in Biostrings objects.
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2024-12-29 |
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bioconductor-bsgenome.mfascicularis.ncbi.5.0
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public |
Full genome sequences for Macaca fascicularis (long-tailed macaque) as provided by NCBI (Macaca_fascicularis_5.0, 2013-06-12) and stored in Biostrings objects.
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2024-12-29 |
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bioconductor-bsgenome.athaliana.tair.tair9
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public |
Full genome sequences for Arabidopsis thaliana as provided by TAIR (TAIR9 Genome Release) and stored in Biostrings objects. Note that TAIR10 is an "annotation release" based on the same genome assembly as TAIR9.
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2024-12-29 |
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bioconductor-methylseekr
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public |
Segmentation of Bis-seq data
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2024-12-29 |
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bioconductor-greylistchip
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public |
Grey Lists -- Mask Artefact Regions Based on ChIP Inputs
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2024-12-29 |
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bioconductor-bsgenome.vvinifera.urgi.iggp12xv0
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public |
Full reference nuclear genome sequences for Vitis vinifera subsp. vinifera PN40024 (derived from Pinot Noir and close to homozygosity after 6-9 rounds of selfing) as assembled by the IGGP (version 12Xv0) and available at the URGI (INRA)
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2024-12-29 |
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bioconductor-sparsesignatures
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public |
SparseSignatures
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2024-12-29 |
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bioconductor-bsgenome.drerio.ucsc.danrer6
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public |
Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer6, Dec. 2008) and stored in Biostrings objects.
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2024-12-29 |
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bioconductor-bsgenome.ggallus.ucsc.galgal4
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public |
Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal4, Nov. 2011) and stored in Biostrings objects.
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2024-12-29 |
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bioconductor-bsgenome.btaurus.ucsc.bostau4
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public |
Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau4, Oct. 2007) and stored in Biostrings objects.
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2024-12-29 |
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bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37
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public |
Extra SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped to reference genome GRCh37.p13 (a patched version of GRCh37 that doesn't alter chromosomes 1-22, X, Y, MT). While the SNPlocs.Hsapiens.dbSNP144.GRCh37 package contains only molecular variations of class "snp", this package contains molecular variations of other classes (in-del, heterozygous, microsatellite, named-locus, no-variation, mixed, and multinucleotide-polymorphism).
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2024-12-29 |
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bioconductor-beat
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public |
BEAT - BS-Seq Epimutation Analysis Toolkit
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2024-12-29 |
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bioconductor-bsgenome.drerio.ucsc.danrer7
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public |
Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer7, Jul. 2010) and stored in Biostrings objects.
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2024-12-29 |
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bioconductor-bsgenome.mfuro.ucsc.musfur1
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public |
Full genome sequences for Mustela putorius furo (Ferret) as provided by UCSC (musFur1, Apr. 2011) and stored in Biostrings objects.
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2024-12-29 |
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bioconductor-bsgenome.tgondii.toxodb.7.0
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public |
Toxoplasma gondii ME49 (ToxoDB-7.0)
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2024-12-29 |
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bioconductor-repitools
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public |
Epigenomic tools
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2024-12-29 |
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bioconductor-bsgenome.mmusculus.ucsc.mm9
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public |
Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects.
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2024-12-29 |
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bioconductor-bsgenome.cfamiliaris.ucsc.canfam3
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public |
Full genome sequences for Canis lupus familiaris (Dog) as provided by UCSC (canFam3, Sep. 2011) and stored in Biostrings objects.
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2024-12-29 |
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bioconductor-bsgenome.ggallus.ucsc.galgal3
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public |
Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal3, May 2006) and stored in Biostrings objects.
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2024-12-29 |
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bioconductor-chipanalyser
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public |
ChIPanalyser: Predicting Transcription Factor Binding Sites
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2024-12-29 |
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bioconductor-bsgenome.rnorvegicus.ucsc.rn6
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public |
Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn6, Jul. 2014) and stored in Biostrings objects.
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2024-12-29 |
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bioconductor-snplocs.hsapiens.dbsnp149.grch38
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public |
SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 149. The source data files used for this package were created by NCBI between November 8-12, 2016, and contain SNPs mapped to reference genome GRCh38.p7 (a patched version of GRCh38 that doesn't alter chromosomes 1-22, X, Y, MT). Note that these SNPs can be "injected" in BSgenome.Hsapiens.NCBI.GRCh38 or in BSgenome.Hsapiens.UCSC.hg38.
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2024-12-29 |
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bioconductor-bsgenome.ptroglodytes.ucsc.pantro6
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public |
Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro6, Jan. 2018) and stored in Biostrings objects.
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2024-12-29 |
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bioconductor-bsgenome.amellifera.ucsc.apimel2
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public |
Full genome sequences for Apis mellifera (Honey Bee) as provided by UCSC (apiMel2, Jan. 2005) and stored in Biostrings objects.
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2024-12-29 |
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bioconductor-bsgenome.alyrata.jgi.v1
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public |
Arabidopsis lyrata full genome (JGI version V1.0)
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2024-12-29 |
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bioconductor-crisprseek
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public |
Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems
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2024-12-29 |
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bioconductor-rgadem
|
public |
de novo motif discovery
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2024-12-29 |
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bioconductor-bsgenome.hsapiens.ncbi.grch38
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public |
Full genome sequences for Homo sapiens (Human) as provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.
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2024-12-29 |
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bioconductor-hiannotator
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public |
Functions for annotating GRanges objects
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2024-12-29 |
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bioconductor-bsgenome.mmusculus.ucsc.mm8
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public |
Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm8, Feb. 2006) and stored in Biostrings objects.
|
2024-12-29 |
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bioconductor-bsgenome.rnorvegicus.ucsc.rn4
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public |
Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn4, Nov. 2004) and stored in Biostrings objects.
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2024-12-29 |
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bioconductor-bsgenome.hsapiens.ucsc.hg17
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public |
Full genome sequences for Homo sapiens (UCSC version hg17)
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2024-12-29 |
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bioconductor-trnascanimport
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public |
Importing a tRNAscan-SE result file as GRanges object
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2024-12-29 |
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bioconductor-bsgenome.athaliana.tair.04232008
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public |
Full genome sequences for Arabidopsis thaliana as provided by TAIR (snapshot from April 23, 2008) and stored in Biostrings objects.
|
2024-12-29 |
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bioconductor-bsgenome.mmulatta.ucsc.rhemac3
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public |
Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac3, Oct. 2010) and stored in Biostrings objects.
|
2024-12-29 |
|
bioconductor-bsgenome.dmelanogaster.ucsc.dm2
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public |
Full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm2, Apr. 2004) and stored in Biostrings objects.
|
2024-12-29 |
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bioconductor-bsgenome.dmelanogaster.ucsc.dm6
|
public |
Full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm6, Aug. 2014) and stored in Biostrings objects.
|
2024-12-29 |
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bioconductor-bsgenome.ptroglodytes.ucsc.pantro2
|
public |
Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro2, Mar. 2006) and stored in Biostrings objects.
|
2024-12-29 |
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bioconductor-rtrmui
|
public |
A shiny user interface for rTRM
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2024-12-29 |
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bioconductor-txdb.athaliana.biomart.plantsmart28
|
public |
Exposes an annotation databases generated from BioMart by exposing these as TxDb objects
|
2024-12-29 |
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bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene
|
public |
Annotation package for TxDb object(s)
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2024-12-29 |
|
bioconductor-epivizrstandalone
|
public |
Run Epiviz Interactive Genomic Data Visualization App within R
|
2024-12-29 |
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bioconductor-epivizr
|
public |
R Interface to epiviz web app
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2024-12-29 |
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bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene
|
public |
Exposes an annotation databases generated from UCSC by exposing these as TxDb objects
|
2024-12-29 |
