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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.
the R package BioNAR, developed to step by step analysis of PPI network. The aim is to quantify and rank each protein’s simultaneous impact into multiple complexes based on network topology and clustering. Package also enables estimating of co-occurrence of diseases across the network and specific clusters pointing towards shared/common mechanisms.
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).
This package provides tools to normalize (several) Hi-C data from replicates.
Full genome sequences for Sus scrofa (Pig) as provided by UCSC (susScr3, Aug. 2011) and stored in Biostrings objects.
Full genome sequences for Glycine max as provided by NCBI (assembly Glycine_max_v4.0, assembly accession GCF_000004515.5) and stored in Biostrings objects.
Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal5, Dec. 2015) and stored in Biostrings objects.
Full genome sequences for Pan paniscus (Bonobo) as provided by UCSC (panPan1, May 2012) and stored in Biostrings objects.
Use hail via basilisk when appropriate, or via reticulate. This package can be used in terra.bio to interact with UK Biobank resources processed by hail.is.
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 Caenorhabditis elegans (Worm) as provided by UCSC (ce2, Mar. 2004) and stored in Biostrings objects.
Example whole genome bisulfite data for the bsseq package.
Inference of ligand-receptor (LR) interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics. BulkSignalR bases its inferences on the LRdb database included in our other package, SingleCellSignalR available from Bioconductor. It relies on a statistical model that is specific to bulk data sets. Different visualization and data summary functions are proposed to help navigating prediction results.
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.
Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau3, Aug. 2006) and stored in Biostrings objects.
Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro6, Jan. 2018) and stored in Biostrings objects.
This package provides a package containing an environment representing the Bovine.cdf file.
Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac10, Feb. 2019) and stored in Biostrings objects.
Saccharomyces cerevisiae (Yeast) full genome as provided by UCSC (sacCer2, June 2008) 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 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).
Full genome sequences for Monodelphis domestica (Opossum) as provided by UCSC (monDom5, Oct. 2006) and stored in Biostrings objects.
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 Bsubtilis\_probe\_tab.
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.