Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer5, Jul. 2007) and stored in Biostrings objects. The sequences are the same as in BSgenome.Drerio.UCSC.danRer5, 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.

Microarray analysis methods that use BufferedMatrix objects.

Full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce2, Mar. 2004) and stored in Biostrings objects.

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.

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.

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.

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.

This package provides a package that allows interactive exploration of AnnotationHub and ExperimentHub resources. It uses DT / DataTable to display resources for multiple organisms. It provides template code for reproducibility and for downloading resources via the indicated Hub package.

Raw data objects used to estimate saliva cell proportion estimates in ewastools. The FlowSorted.Saliva.EPIC object is constructed from samples assayed by Lauren Middleton et. al. (2021).

Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau6, Nov. 2009) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau6, 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.

Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac2, Jan. 2006) and stored in Biostrings objects.

Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal3, May 2006) and stored in Biostrings objects.

Full genome sequences for Pan paniscus (Bonobo) as provided by UCSC (panPan2, Dec. 2015) and stored in Biostrings objects.

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.

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.

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Bovine\_probe\_tab.

This package provides a BiocBook can be created by authors (e.g. R developers, but also scientists, teachers, communicators, ...) who wish to 1) write (compile a body of biological and/or bioinformatics knowledge), 2) containerize (provide Docker images to reproduce the examples illustrated in the compendium), 3) publish (deploy an online book to disseminate the compendium), and 4) version (automatically generate specific online book versions and Docker images for specific Bioconductor releases).

Full genome sequences for Apis mellifera as provided by NCBI (assembly Amel_HAv3.1, assembly accession GCF_003254395.2) and stored in Biostrings objects.

The package provides a bioimage dataset for the image analysis using machine learning and deep learning. The dataset includes microscopy imaging data with supervised labels. The data is provided as R list data that can be loaded to Keras/tensorflow in R.

bugphyzz is an electronic database of standardized microbial annotations. It facilitates the creation of microbial signatures based on shared attributes, which are utilized for bug set enrichment analysis. The data also includes annotations imputed with ancestra state reconstruction methods.

Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro3, Oct. 2010) and stored in Biostrings objects.

Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg17, May 2004) and stored in Biostrings objects.

Full genome sequences for Chlamydomonas reinhardtii (v5.6) as provided by JGI and stored in Biostrings objects. The data in this package is public. See citation("BSgenome.Creinhardtii.JGI.v5.6") for how to cite in publications.

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.