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r-bsgenome-hsapiens-ucsc-hg18-masked 1.3.99
Propagated dependencies: r-bsgenome-hsapiens-ucsc-hg18@1.3.1000 r-bsgenome@1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg18.masked
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full masked genome sequences for Homo sapiens (UCSC version hg18)
Description:

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.

r-bedbaser 1.2.6
Propagated dependencies: r-tidyr@1.3.1 r-tibble@3.3.0 r-stringr@1.6.0 r-rtracklayer@1.70.0 r-rlang@1.1.6 r-r-utils@2.13.0 r-purrr@1.2.0 r-httr@1.4.7 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-dplyr@1.1.4 r-curl@7.0.0 r-biocfilecache@3.0.0 r-anvil@1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://github.com/waldronlab/bedbaser
Licenses: FSDG-compatible
Build system: r
Synopsis: BEDbase client
Description:

This package provides a client for BEDbase. bedbaser provides access to the API at api.bedbase.org. It also includes convenience functions to import BED files into GRanges objects and BEDsets into GRangesLists.

r-bsgenome-ptroglodytes-ucsc-pantro5 1.4.2
Propagated dependencies: r-bsgenome@1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://bioconductor.org/packages/BSgenome.Ptroglodytes.UCSC.panTro5
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full genome sequences for Pan troglodytes (UCSC version panTro5)
Description:

Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro5, May 2016) and stored in Biostrings objects.

r-bsgenome-drerio-ucsc-danrer6-masked 1.3.99
Propagated dependencies: r-bsgenome-drerio-ucsc-danrer6@1.4.0 r-bsgenome@1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://bioconductor.org/packages/BSgenome.Drerio.UCSC.danRer6.masked
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full masked genome sequences for Danio rerio (UCSC version danRer6)
Description:

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.

r-bumhmm 1.34.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-stringi@1.8.7 r-iranges@2.44.0 r-gtools@3.9.5 r-devtools@2.4.6 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://bioconductor.org/packages/BUMHMM
Licenses: GPL 3
Build system: r
Synopsis: Computational pipeline for computing probability of modification from structure probing experiment data
Description:

This is a probabilistic modelling pipeline for computing per- nucleotide posterior probabilities of modification from the data collected in structure probing experiments. The model supports multiple experimental replicates and empirically corrects coverage- and sequence-dependent biases. The model utilises the measure of a "drop-off rate" for each nucleotide, which is compared between replicates through a log-ratio (LDR). The LDRs between control replicates define a null distribution of variability in drop-off rate observed by chance and LDRs between treatment and control replicates gets compared to this distribution. Resulting empirical p-values (probability of being "drawn" from the null distribution) are used as observations in a Hidden Markov Model with a Beta-Uniform Mixture model used as an emission model. The resulting posterior probabilities indicate the probability of a nucleotide of having being modified in a structure probing experiment.

r-bugphyzz 1.4.0
Propagated dependencies: r-tidyselect@1.2.1 r-tidyr@1.3.1 r-stringr@1.6.0 r-s4vectors@0.48.0 r-purrr@1.2.0 r-httr2@1.2.1 r-dplyr@1.1.4 r-biocfilecache@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://github.com/waldronlab/bugphyzz
Licenses: Artistic License 2.0
Build system: r
Synopsis: harmonized data resource and software for enrichment analysis of microbial physiologies
Description:

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.

r-bsgenome-celegans-ucsc-ce11 1.4.2
Propagated dependencies: r-bsgenome@1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://bioconductor.org/packages/BSgenome.Celegans.UCSC.ce11
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full genome sequences for Caenorhabditis elegans (UCSC version ce11)
Description:

Full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce11, Feb. 2013) and stored in Biostrings objects.

r-bsgenome-carietinum-ncbi-v1 1.0.0
Propagated dependencies: r-bsgenome@1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://bioconductor.org/packages/BSgenome.Carietinum.NCBI.v1
Licenses: GPL 3
Build system: r
Synopsis: Cicer arietinum (Chickpea) full genome (NCBI version ASM33114v1)
Description:

Full genome sequences for Cicer arietinum (Chickpea) as provided by NCBI (ASM33114v1, Jan. 2013) and stored in Biostrings objects.

r-bsgenome-tgondii-toxodb-7-0 0.99.1
Propagated dependencies: r-bsgenome@1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://bioconductor.org/packages/BSgenome.Tgondii.ToxoDB.7.0
Licenses: FSDG-compatible
Build system: r
Synopsis: Toxoplasma gondii ME49 (ToxoDB-7.0)
Description:

Toxoplasma gondii ME49 genome Release 7.0 available at http://www.toxodb.org.

r-bsgenome-cjacchus-ucsc-caljac4 1.5.0
Propagated dependencies: r-bsgenome@1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://bioconductor.org/packages/BSgenome.Cjacchus.UCSC.calJac4
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full genome sequences for Callithrix jacchus (UCSC version calJac4)
Description:

Full genome sequences for Callithrix jacchus (Marmoset) as provided by UCSC (calJac4, May 2020) and wrapped in a BSgenome object.

r-bsgenome-mmulatta-ucsc-rhemac3 1.4.0
Propagated dependencies: r-bsgenome@1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://bioconductor.org/packages/BSgenome.Mmulatta.UCSC.rheMac3
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full genome sequences for Macaca mulatta (UCSC version rheMac3)
Description:

Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac3, Oct. 2010) and stored in Biostrings objects.

r-bsgenome-amellifera-ucsc-apimel2-masked 1.3.99
Propagated dependencies: r-bsgenome-amellifera-ucsc-apimel2@1.4.0 r-bsgenome@1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://bioconductor.org/packages/BSgenome.Amellifera.UCSC.apiMel2.masked
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full masked genome sequences for Apis mellifera (UCSC version apiMel2)
Description:

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.

r-bsgenome-tguttata-ucsc-taegut2 1.4.2
Propagated dependencies: r-bsgenome@1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://bioconductor.org/packages/BSgenome.Tguttata.UCSC.taeGut2
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full genome sequences for Taeniopygia guttata (UCSC version taeGut2)
Description:

Full genome sequences for Taeniopygia guttata (Zebra finch) as provided by UCSC (taeGut2, Feb. 2013) and stored in Biostrings objects.

r-beta7 1.48.0
Propagated dependencies: r-marray@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://bioconductor.org/packages/beta7
Licenses: LGPL 2.0+
Build system: r
Synopsis: Rodriguez et al. (2004) Differential Gene Expression by Memory/Effector T Helper Cells Bearing the Gut-Homing Receptor Integrin alpha4 beta7
Description:

Data from 6 gpr files aims to identify differential expressed genes between the beta 7+ and beta 7- memory T helper cells.

r-bsgenome-mfascicularis-ncbi-5-0 1.4.2
Propagated dependencies: r-bsgenome@1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://bioconductor.org/packages/BSgenome.Mfascicularis.NCBI.5.0
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full genome sequences for Macaca fascicularis (Macaca_fascicularis_5.0)
Description:

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.

r-beachmat-tiledb 1.2.0
Propagated dependencies: r-tiledbarray@1.20.0 r-tiledb@0.33.0 r-rcpp@1.1.0 r-delayedarray@0.36.0 r-beachmat@2.26.0 r-assorthead@1.4.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://github.com/tatami-inc/beachmat.tiledb
Licenses: GPL 3
Build system: r
Synopsis: beachmat bindings for TileDB-backed matrices
Description:

Extends beachmat to initialize tatami matrices from TileDB-backed arrays. This allows C++ code in downstream packages to directly call the TileDB C/C++ library to access array data, without the need for block processing via DelayedArray. Developers only need to import this package to automatically extend the capabilities of beachmat::initializeCpp to TileDBArray instances.

r-busseq 1.16.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-s4vectors@0.48.0 r-gplots@3.2.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://github.com/songfd2018/BUSseq
Licenses: Artistic License 2.0
Build system: r
Synopsis: Batch Effect Correction with Unknow Subtypes for scRNA-seq data
Description:

BUSseq R package fits an interpretable Bayesian hierarchical model---the Batch Effects Correction with Unknown Subtypes for scRNA seq Data (BUSseq)---to correct batch effects in the presence of unknown cell types. BUSseq is able to simultaneously correct batch effects, clusters cell types, and takes care of the count data nature, the overdispersion, the dropout events, and the cell-specific sequencing depth of scRNA-seq data. After correcting the batch effects with BUSseq, the corrected value can be used for downstream analysis as if all cells were sequenced in a single batch. BUSseq can integrate read count matrices obtained from different scRNA-seq platforms and allow cell types to be measured in some but not all of the batches as long as the experimental design fulfills the conditions listed in our manuscript.

r-bsgenome-hsapiens-ncbi-t2t-chm13v2-0 1.5.0
Propagated dependencies: r-bsgenome@1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://bioconductor.org/packages/BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0
Licenses: Artistic License 2.0
Build system: r
Synopsis: T2T-CHM13v2.0 assembly (Homo sapiens) wrapped in a BSgenome object
Description:

The T2T-CHM13v2.0 assembly (accession GCA_009914755.4), as submitted to NCBI by the T2T Consortium, and wrapped in a BSgenome object. Companion paper: "The complete sequence of a human genome" by Nurk S, Koren S, Rhie A, Rautiainen M, et al. Science, 2022.

r-bsseqdata 0.48.0
Propagated dependencies: r-bsseq@1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://bioconductor.org/packages/bsseqData
Licenses: Artistic License 2.0
Build system: r
Synopsis: Example whole genome bisulfite data for the bsseq package
Description:

Example whole genome bisulfite data for the bsseq package.

r-bsgenome-hsapiens-ucsc-hg17-masked 1.3.999
Propagated dependencies: r-bsgenome-hsapiens-ucsc-hg17@1.3.1001 r-bsgenome@1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg17.masked
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full masked genome sequences for Homo sapiens (UCSC version hg17)
Description:

Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg17, May 2004) and stored in Biostrings objects. The sequences are the same as in BSgenome.Hsapiens.UCSC.hg17, 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.

r-bsgenome-cfamiliaris-ucsc-canfam2 1.4.0
Propagated dependencies: r-bsgenome@1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://bioconductor.org/packages/BSgenome.Cfamiliaris.UCSC.canFam2
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full genome sequences for Canis lupus familiaris (UCSC version canFam2)
Description:

Full genome sequences for Canis lupus familiaris (Dog) as provided by UCSC (canFam2, May 2005) and stored in Biostrings objects.

r-bsgenome-amellifera-beebase-assembly4 1.4.0
Propagated dependencies: r-bsgenome@1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://bioconductor.org/packages/BSgenome.Amellifera.BeeBase.assembly4
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full genome sequences for Apis mellifera (BeeBase assembly4)
Description:

iFull genome sequences for Apis mellifera (Honey Bee) as provided by BeeBase (assembly4, Feb. 2008) and stored in Biostrings objects.

r-bnem 1.18.0
Propagated dependencies: r-vsn@3.78.0 r-sva@3.58.0 r-snowfall@1.84-6.3 r-rmarkdown@2.30 r-rgraphviz@2.54.0 r-rcolorbrewer@1.1-3 r-mnem@1.26.0 r-matrixstats@1.5.0 r-limma@3.66.0 r-graph@1.88.0 r-flexclust@1.5.0 r-epinem@1.34.0 r-cluster@2.1.8.1 r-cellnoptr@1.56.0 r-biobase@2.70.0 r-binom@1.1-1.1 r-affy@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://github.com/MartinFXP/bnem/
Licenses: GPL 3
Build system: r
Synopsis: Training of logical models from indirect measurements of perturbation experiments
Description:

bnem combines the use of indirect measurements of Nested Effects Models (package mnem) with the Boolean networks of CellNOptR. Perturbation experiments of signalling nodes in cells are analysed for their effect on the global gene expression profile. Those profiles give evidence for the Boolean regulation of down-stream nodes in the network, e.g., whether two parents activate their child independently (OR-gate) or jointly (AND-gate).

r-bandle 1.14.0
Propagated dependencies: r-tidyr@1.3.1 r-s4vectors@0.48.0 r-robustbase@0.99-6 r-rlang@1.1.6 r-rcpparmadillo@15.2.2-1 r-rcpp@1.1.0 r-rcolorbrewer@1.1-3 r-prolocdata@1.48.0 r-proloc@1.50.0 r-plyr@1.8.9 r-msnbase@2.36.0 r-lbfgs@1.2.1.2 r-knitr@1.50 r-gtools@3.9.5 r-gridextra@2.3 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-ggalluvial@0.12.5 r-dplyr@1.1.4 r-coda@0.19-4.1 r-circlize@0.4.16 r-biocstyle@2.38.0 r-biocparallel@1.44.0 r-biobase@2.70.0 r-bh@1.87.0-1
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: http://github.com/ococrook/bandle
Licenses: Artistic License 2.0
Build system: r
Synopsis: An R package for the Bayesian analysis of differential subcellular localisation experiments
Description:

The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data. Experimental methods supported include dynamic LOPIT-DC, hyperLOPIT, Dynamic Organellar Maps, Dynamic PCP. It provides Bioconductor infrastructure to analyse these data.

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