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bioconductor-basic4cseq
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public |
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
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2024-12-31 |
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bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked
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public |
Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac2, Jan. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmulatta.UCSC.rheMac2, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default. NOTE: In most assemblies available at UCSC, Tandem Repeats Finder repeats were filtered to retain only the repeats with period <= 12. However, the filtering was omitted for this assembly, so the TRF masks contain all Tandem Repeats Finder results.
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2024-12-31 |
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bioconductor-bsgenome.hsapiens.ucsc.hg18.masked
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public |
Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg18, Mar. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Hsapiens.UCSC.hg18, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-vanillaice
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public |
A Hidden Markov Model for high throughput genotyping arrays
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2024-12-31 |
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bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked
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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. The sequences are the same as in BSgenome.Cfamiliaris.UCSC.canFam2, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked
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public |
Full genome sequences for Sus scrofa (Pig) as provided by UCSC (susScr3, Aug. 2011) and stored in Biostrings objects. The sequences are the same as in BSgenome.Sscrofa.UCSC.susScr3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-flowsorted.blood.epic
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public |
Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells
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2024-12-31 |
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bioconductor-tfbstools
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public |
Software Package for Transcription Factor Binding Site (TFBS) Analysis
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2024-12-31 |
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bioconductor-hdf5array
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public |
HDF5 datasets as array-like objects in R
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2024-12-31 |
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bioconductor-bsgenome.drerio.ucsc.danrer6.masked
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public |
Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer6, Dec. 2008) and stored in Biostrings objects. The sequences are the same as in BSgenome.Drerio.UCSC.danRer6, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-bsgenome.ggallus.ucsc.galgal4.masked
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public |
Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal4, Nov. 2011) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ggallus.UCSC.galGal4, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-bsgenome.btaurus.ucsc.bostau4.masked
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public |
Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau4, Oct. 2007) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau4, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-bsgenome.drerio.ucsc.danrer7.masked
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public |
Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer7, Jul. 2010) and stored in Biostrings objects. The sequences are the same as in BSgenome.Drerio.UCSC.danRer7, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-cleanupdtseq
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public |
cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data
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2024-12-31 |
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bioconductor-bsgenome.mmusculus.ucsc.mm9.masked
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public |
Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked
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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. The sequences are the same as in BSgenome.Cfamiliaris.UCSC.canFam3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-bsgenome.ggallus.ucsc.galgal3.masked
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public |
Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal3, May 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ggallus.UCSC.galGal3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-bsgenome.amellifera.ucsc.apimel2.masked
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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. The sequences are the same as in BSgenome.Amellifera.UCSC.apiMel2, except that each of them has the 3 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), and (3) the mask of repeats from RepeatMasker (RM mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-hireadsprocessor
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public |
Functions to process LM-PCR reads from 454/Illumina data
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2024-12-31 |
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bioconductor-bsgenome.mmusculus.ucsc.mm8.masked
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public |
Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm8, Feb. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmusculus.UCSC.mm8, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked
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public |
Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn4, Nov. 2004) and stored in Biostrings objects. The sequences are the same as in BSgenome.Rnorvegicus.UCSC.rn4, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-bsgenome.hsapiens.ucsc.hg17.masked
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public |
Full masked genome sequences for Homo sapiens (UCSC version hg17)
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2024-12-31 |
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bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked
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public |
Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac3, Oct. 2010) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmulatta.UCSC.rheMac3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked
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public |
Full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm2, Apr. 2004) and stored in Biostrings objects. The sequences are the same as in BSgenome.Dmelanogaster.UCSC.dm2, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked
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public |
Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro2, Mar. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ptroglodytes.UCSC.panTro2, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.
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2024-12-31 |
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bioconductor-ensdb.rnorvegicus.v79
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public |
Exposes an annotation databases generated from Ensembl.
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2024-12-31 |
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r-locuszoomr
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public |
Publication-ready regional gene locus plots similar to those produced by the web interface 'LocusZoom' <https://my.locuszoom.org>, but running locally in R. Genetic or genomic data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly', allowing flexibility and easy customisation including laying out multiple locus plots on the same page. It uses the 'LDlink' API <https://ldlink.nih.gov/?tab=apiaccess> to query linkage disequilibrium data from the 1000 Genomes Project and can overlay this on plots.
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2024-12-31 |
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bioconductor-ensdb.rnorvegicus.v75
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public |
Exposes an annotation databases generated from Ensembl.
|
2024-12-31 |
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bioconductor-ensdb.mmusculus.v75
|
public |
Exposes an annotation databases generated from Ensembl.
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2024-12-31 |
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bioconductor-ensdb.hsapiens.v86
|
public |
Exposes an annotation databases generated from Ensembl.
|
2024-12-31 |
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bioconductor-ensdb.hsapiens.v79
|
public |
Exposes an annotation databases generated from Ensembl.
|
2024-12-31 |
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bioconductor-ensdb.hsapiens.v75
|
public |
Exposes an annotation databases generated from Ensembl.
|
2024-12-31 |
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bioconductor-ensdb.mmusculus.v79
|
public |
Exposes an annotation databases generated from Ensembl.
|
2024-12-31 |
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bioconductor-scrnaseq
|
public |
Collection of Public Single-Cell RNA-Seq Datasets
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2024-12-31 |
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bioconductor-clipper
|
public |
Gene Set Analysis Exploiting Pathway Topology
|
2024-12-31 |
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bioconductor-damirseq
|
public |
Data Mining for RNA-seq data: normalization, feature selection and classification
|
2024-12-31 |
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bioconductor-ruvseq
|
public |
Remove Unwanted Variation from RNA-Seq Data
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2024-12-31 |
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bioconductor-rnaeditr
|
public |
Statistical analysis of RNA editing sites and hyper-editing regions
|
2024-12-31 |
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bioconductor-minfi
|
public |
Analyze Illumina Infinium DNA methylation arrays
|
2024-12-31 |
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bioconductor-cogito
|
public |
Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets
|
2024-12-31 |
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bioconductor-agimicrorna
|
public |
Processing and Differential Expression Analysis of Agilent microRNA chips
|
2024-12-31 |
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bioconductor-gnosis
|
public |
Genomics explorer using statistical and survival analysis in R
|
2024-12-31 |
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bioconductor-affycoretools
|
public |
Functions useful for those doing repetitive analyses with Affymetrix GeneChips
|
2024-12-31 |
|
bioconductor-cancer
|
public |
A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC
|
2024-12-31 |
|
bioconductor-reportingtools
|
public |
Tools for making reports in various formats
|
2024-12-31 |
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bioconductor-chipseq
|
public |
chipseq: A package for analyzing chipseq data
|
2024-12-30 |
|
bioconductor-cbaf
|
public |
Automated functions for comparing various omic data from cbioportal.org
|
2024-12-30 |
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bioconductor-girafe
|
public |
Genome Intervals and Read Alignments for Functional Exploration
|
2024-12-30 |
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bioconductor-scp
|
public |
Mass Spectrometry-Based Single-Cell Proteomics Data Analysis
|
2024-12-30 |
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bioconductor-chipseqr
|
public |
Identifying Protein Binding Sites in High-Throughput Sequencing Data
|
2024-12-30 |
