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bioconductor-methylinheritance
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public |
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect
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2024-12-30 |
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bioconductor-rjmcmcnucleosomes
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public |
Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)
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2024-12-30 |
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bioconductor-bsgenome.hsapiens.ucsc.hg19
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public |
Full genome sequences for Homo sapiens (UCSC version hg19, based on GRCh37.p13)
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2024-12-30 |
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bioconductor-redseq
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public |
Analysis of high-throughput sequencing data processed by restriction enzyme digestion
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2024-12-30 |
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bioconductor-bsgenome.scerevisiae.ucsc.saccer1
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public |
Saccharomyces cerevisiae (Yeast) full genome as provided by UCSC (sacCer1, Oct. 2003) and stored in Biostrings objects.
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2024-12-30 |
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bioconductor-guideseq
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public |
GUIDE-seq and PEtag-seq analysis pipeline
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2024-12-30 |
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bioconductor-annotatr
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public |
Annotation of Genomic Regions to Genomic Annotations
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2024-12-30 |
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bioconductor-chippeakanno
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public |
Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data
|
2024-12-30 |
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bioconductor-methylpipe
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public |
Base resolution DNA methylation data analysis
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2024-12-30 |
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bioconductor-gothic
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public |
Binomial test for Hi-C data analysis
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2024-12-30 |
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bioconductor-bsgenome.vvinifera.urgi.iggp8x
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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 8X) and available at the URGI (INRA). More details in Jaillon et al (Nature, 2007).
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2024-12-30 |
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bioconductor-bsgenome.rnorvegicus.ucsc.rn5
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public |
Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn5, Mar. 2012) and stored in Biostrings objects.
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2024-12-30 |
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bioconductor-genomation
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public |
Summary, annotation and visualization of genomic data
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2024-12-30 |
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bioconductor-bsgenome.btaurus.ucsc.bostau3
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public |
Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau3, Aug. 2006) and stored in Biostrings objects.
|
2024-12-30 |
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bioconductor-regioner
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public |
Association analysis of genomic regions based on permutation tests
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2024-12-30 |
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bioconductor-bsgenome.celegans.ucsc.ce11
|
public |
Full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce11, Feb. 2013) and stored in Biostrings objects.
|
2024-12-30 |
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bioconductor-gcapc
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public |
GC Aware Peak Caller
|
2024-12-30 |
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bioconductor-bsgenome.ptroglodytes.ucsc.pantro3
|
public |
Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro3, Oct. 2010) and stored in Biostrings objects.
|
2024-12-30 |
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bioconductor-bsgenome.celegans.ucsc.ce6
|
public |
Full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings objects.
|
2024-12-30 |
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bioconductor-bsgenome.amellifera.beebase.assembly4
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public |
iFull genome sequences for Apis mellifera (Honey Bee) as provided by BeeBase (assembly4, Feb. 2008) and stored in Biostrings objects.
|
2024-12-30 |
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bioconductor-bsgenome.ptroglodytes.ucsc.pantro5
|
public |
Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro5, May 2016) and stored in Biostrings objects.
|
2024-12-30 |
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bioconductor-bsgenome.hsapiens.1000genomes.hs37d5
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public |
1000genomes Phase2 Reference Genome Sequence (hs37d5), based on NCBI GRCh37.
|
2024-12-30 |
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bioconductor-bsgenome.btaurus.ucsc.bostau8
|
public |
Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau8, Jun. 2014) and stored in Biostrings objects.
|
2024-12-30 |
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bioconductor-bsgenome.hsapiens.ucsc.hg38
|
public |
Full genomic sequences for Homo sapiens (UCSC genome hg38)
|
2024-12-30 |
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bioconductor-bsgenome.drerio.ucsc.danrer10
|
public |
Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer10, Sep. 2014) and stored in Biostrings objects.
|
2024-12-30 |
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bioconductor-bsgenome.drerio.ucsc.danrer5
|
public |
Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer5, Jul. 2007) and stored in Biostrings objects.
|
2024-12-30 |
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bioconductor-bsgenome.dmelanogaster.ucsc.dm3
|
public |
Full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm3, Apr. 2006) and stored in Biostrings objects.
|
2024-12-30 |
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bioconductor-bsgenome.mmusculus.ucsc.mm10
|
public |
Full genome sequences for Mus musculus (UCSC version mm10, based on GRCm38.p6)
|
2024-12-30 |
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bioconductor-bsgenome.mmulatta.ucsc.rhemac8
|
public |
Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac8, Nov. 2015) and stored in Biostrings objects.
|
2024-12-29 |
|
bioconductor-bsgenome.vvinifera.urgi.iggp12xv2
|
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 12Xv2) and available at the URGI (INRA)
|
2024-12-29 |
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bioconductor-bsgenome.scerevisiae.ucsc.saccer3
|
public |
Saccharomyces cerevisiae (Yeast) full genome as provided by UCSC (sacCer3, April 2011) and stored in Biostrings objects.
|
2024-12-29 |
|
bioconductor-bsgenome.btaurus.ucsc.bostau6
|
public |
Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau6, Nov. 2009) and stored in Biostrings objects.
|
2024-12-29 |
|
bioconductor-bsgenome.tguttata.ucsc.taegut1
|
public |
Full genome sequences for Taeniopygia guttata (Zebra finch) as provided by UCSC (taeGut1, Jul. 2008) and stored in Biostrings objects.
|
2024-12-29 |
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bioconductor-bsgenome.sscrofa.ucsc.susscr11
|
public |
Full genome sequences for Sus scrofa (Pig) as provided by UCSC (susScr11, Feb. 2017) and stored in Biostrings objects.
|
2024-12-29 |
|
bioconductor-bsgenome.tguttata.ucsc.taegut2
|
public |
Full genome sequences for Taeniopygia guttata (Zebra finch) as provided by UCSC (taeGut2, Feb. 2013) and stored in Biostrings objects.
|
2024-12-29 |
|
bioconductor-bsgenome.gaculeatus.ucsc.gasacu1
|
public |
Full genome sequences for Gasterosteus aculeatus (Stickleback) as provided by UCSC (gasAcu1, Feb. 2006) and stored in Biostrings objects.
|
2024-12-29 |
|
bioconductor-bsgenome.ecoli.ncbi.20080805
|
public |
Escherichia coli full genomes for several strains as provided by NCBI on 2008/08/05 and stored in Biostrings objects.
|
2024-12-29 |
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bioconductor-biovizbase
|
public |
Basic graphic utilities for visualization of genomic data.
|
2024-12-29 |
|
bioconductor-methylkit
|
public |
DNA methylation analysis from high-throughput bisulfite sequencing results
|
2024-12-29 |
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bioconductor-qsea
|
public |
IP-seq data analysis and vizualization
|
2024-12-29 |
|
bioconductor-bsgenome.scerevisiae.ucsc.saccer2
|
public |
Saccharomyces cerevisiae (Yeast) full genome as provided by UCSC (sacCer2, June 2008) and stored in Biostrings objects.
|
2024-12-29 |
|
bioconductor-bsgenome.mmulatta.ucsc.rhemac2
|
public |
Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac2, Jan. 2006) and stored in Biostrings objects.
|
2024-12-29 |
|
bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38
|
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 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). While the SNPlocs.Hsapiens.dbSNP144.GRCh38 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).
|
2024-12-29 |
|
bioconductor-bsgenome.aofficinalis.ncbi.v1
|
public |
Full genome sequences for Asparagus officinalis (Garden asparagus) as provided by NCBI (Aspof.V1, Feb. 2017) and stored in Biostrings objects.
|
2024-12-29 |
|
bioconductor-bsgenome.hsapiens.ucsc.hg18
|
public |
Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg18, Mar. 2006) and stored in Biostrings objects.
|
2024-12-29 |
|
bioconductor-snplocs.hsapiens.dbsnp150.grch38
|
public |
SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 150. The source data files used for this package were created by NCBI between March 12-14, 2017, 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.
|
2024-12-29 |
|
bioconductor-bsgenome.osativa.msu.msu7
|
public |
Oryza sativa full genome (MSU7)
|
2024-12-29 |
|
bioconductor-bsgenome.celegans.ucsc.ce2
|
public |
Full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce2, Mar. 2004) and stored in Biostrings objects.
|
2024-12-29 |
|
bioconductor-bsgenome.ggallus.ucsc.galgal5
|
public |
Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal5, Dec. 2015) and stored in Biostrings objects.
|
2024-12-29 |
|
bioconductor-bsgenome.carietinum.ncbi.v1
|
public |
Full genome sequences for Cicer arietinum (Chickpea) as provided by NCBI (ASM33114v1, Jan. 2013) and stored in Biostrings objects.
|
2024-12-29 |
