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bioconductor-bsgenome.cjacchus.ucsc.caljac3
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public |
Full genome sequences for Callithrix jacchus (Marmoset) as provided by UCSC (calJac3, Mar. 2009) and stored in Biostrings objects.
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2024-12-29 |
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bioconductor-bsgenome.ggallus.ucsc.galgal5
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public |
Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal5, Dec. 2015) and stored in Biostrings objects.
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2024-12-29 |
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bioconductor-bsgenome.gmax.ncbi.gmv40
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public |
Full genome sequences for Glycine max (Gmv40)
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2024-12-29 |
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bioconductor-bsgenome.carietinum.ncbi.v1
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public |
Full genome sequences for Cicer arietinum (Chickpea) as provided by NCBI (ASM33114v1, Jan. 2013) and stored in Biostrings objects.
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2024-12-29 |
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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.cneoformansvargrubiikn99.ncbi.asm221672v1
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public |
Full Genome Sequence for Cryptococcus neoformans var. grubii KN99 (ASM221672v1)
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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.amellifera.ncbi.amelhav3.1
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public |
Full genome sequences for Apis mellifera (Amel_HAv3.1)
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2024-12-29 |
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bioconductor-bsgenome.mfascicularis.ncbi.5.0
|
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.
|
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-periodicdna
|
public |
Set of tools to identify periodic occurrences of k-mers in DNA sequences
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2024-12-29 |
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bioconductor-methylseekr
|
public |
Segmentation of Bis-seq data
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2024-12-29 |
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bioconductor-greylistchip
|
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
|
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
|
public |
SparseSignatures
|
2024-12-29 |
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bioconductor-pipeframe
|
public |
Pipeline framework for bioinformatics in R
|
2024-12-29 |
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bioconductor-bsgenome.drerio.ucsc.danrer6
|
public |
Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer6, Dec. 2008) and stored in Biostrings objects.
|
2024-12-29 |
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bioconductor-bsgenome.ggallus.ucsc.galgal6
|
public |
Full genome sequences for Gallus gallus (UCSC version galGal6)
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2024-12-29 |
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bioconductor-crisprbowtie
|
public |
Bowtie-based alignment of CRISPR gRNA spacer sequences
|
2024-12-29 |
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bioconductor-bsgenome.ggallus.ucsc.galgal4
|
public |
Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal4, Nov. 2011) and stored in Biostrings objects.
|
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.
|
2024-12-29 |
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bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37
|
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
|
public |
BEAT - BS-Seq Epimutation Analysis Toolkit
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2024-12-29 |
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r-dpeak
|
public |
This package provides functions for fitting dPeak, a statistical framework to deconvolve ChIP-seq peaks.
|
2024-12-29 |
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bioconductor-bsgenome.drerio.ucsc.danrer7
|
public |
Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer7, Jul. 2010) and stored in Biostrings objects.
|
2024-12-29 |
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bioconductor-bsgenome.mfuro.ucsc.musfur1
|
public |
Full genome sequences for Mustela putorius furo (Ferret) as provided by UCSC (musFur1, Apr. 2011) and stored in Biostrings objects.
|
2024-12-29 |
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bioconductor-bsgenome.tgondii.toxodb.7.0
|
public |
Toxoplasma gondii ME49 (ToxoDB-7.0)
|
2024-12-29 |
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bioconductor-repitools
|
public |
Epigenomic tools
|
2024-12-29 |
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bioconductor-bsgenome.mmusculus.ucsc.mm9
|
public |
Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects.
|
2024-12-29 |
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bioconductor-bsgenome.cfamiliaris.ucsc.canfam3
|
public |
Full genome sequences for Canis lupus familiaris (Dog) as provided by UCSC (canFam3, Sep. 2011) and stored in Biostrings objects.
|
2024-12-29 |
|
bioconductor-bsgenome.ggallus.ucsc.galgal3
|
public |
Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal3, May 2006) and stored in Biostrings objects.
|
2024-12-29 |
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bioconductor-cliprofiler
|
public |
A package for the CLIP data visualization
|
2024-12-29 |
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bioconductor-chipanalyser
|
public |
ChIPanalyser: Predicting Transcription Factor Binding Sites
|
2024-12-29 |
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bioconductor-bsgenome.rnorvegicus.ucsc.rn6
|
public |
Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn6, Jul. 2014) and stored in Biostrings objects.
|
2024-12-29 |
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bioconductor-bsgenome.mdomestica.ucsc.mondom5
|
public |
Full genome sequences for Monodelphis domestica (Opossum) as provided by UCSC (monDom5, Oct. 2006) and stored in Biostrings objects.
|
2024-12-29 |
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bioconductor-motif2site
|
public |
Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions
|
2024-12-29 |
|
bioconductor-snplocs.hsapiens.dbsnp149.grch38
|
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.
|
2024-12-29 |
|
bioconductor-bsgenome.ptroglodytes.ucsc.pantro6
|
public |
Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro6, Jan. 2018) and stored in Biostrings objects.
|
2024-12-29 |
|
bioconductor-bsgenome.hsapiens.ucsc.hg38.dbsnp151.minor
|
public |
Full genome sequences for Homo sapiens (UCSC version hg38, based on GRCh38.p12) with injected minor alleles (dbSNP151)
|
2024-12-29 |
|
bioconductor-bsgenome.amellifera.ucsc.apimel2
|
public |
Full genome sequences for Apis mellifera (Honey Bee) as provided by UCSC (apiMel2, Jan. 2005) and stored in Biostrings objects.
|
2024-12-29 |
|
bioconductor-bsgenome.alyrata.jgi.v1
|
public |
Arabidopsis lyrata full genome (JGI version V1.0)
|
2024-12-29 |
|
bioconductor-crisprseek
|
public |
Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems
|
2024-12-29 |
|
bioconductor-xnastring
|
public |
Efficient Manipulation of Modified Oligonucleotide Sequences
|
2024-12-29 |
|
bioconductor-rgadem
|
public |
de novo motif discovery
|
2024-12-29 |
|
bioconductor-bsgenome.hsapiens.ncbi.grch38
|
public |
Full genome sequences for Homo sapiens (Human) as provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.
|
2024-12-29 |
