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r-phosphonormalizer 1.34.0
Propagated dependencies: r-plyr@1.8.9 r-matrixstats@1.5.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/phosphonormalizer
Licenses: GPL 2+
Build system: r
Synopsis: Compensates for the bias introduced by median normalization in
Description:

It uses the overlap between enriched and non-enriched datasets to compensate for the bias introduced in global phosphorylation after applying median normalization.

r-primeviewprobe 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/primeviewprobe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type primeview
Description:

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 PrimeView\_probe\_tab.

r-pd-porcine 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.porcine
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for The Manufacturer's Name Porcine
Description:

Platform Design Info for The Manufacturer's Name Porcine.

r-panp 1.80.0
Propagated dependencies: r-biobase@2.70.0 r-affy@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/panp
Licenses: GPL 2+
Build system: r
Synopsis: Presence-Absence Calls from Negative Strand Matching Probesets
Description:

This package provides a function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date.

r-pd-drosophila-2 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.drosophila.2
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for The Manufacturer's Name Drosophila_2
Description:

Platform Design Info for The Manufacturer's Name Drosophila_2.

r-proactiv 1.20.0
Propagated dependencies: r-txdbmaker@1.6.0 r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-scales@1.4.0 r-s4vectors@0.48.0 r-rlang@1.1.6 r-iranges@2.44.0 r-gplots@3.2.0 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-genomicalignments@1.46.0 r-genomeinfodb@1.46.0 r-dplyr@1.1.4 r-deseq2@1.50.2 r-data-table@1.17.8 r-biocparallel@1.44.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://github.com/GoekeLab/proActiv
Licenses: Expat
Build system: r
Synopsis: Estimate Promoter Activity from RNA-Seq data
Description:

Most human genes have multiple promoters that control the expression of different isoforms. The use of these alternative promoters enables the regulation of isoform expression pre-transcriptionally. Alternative promoters have been found to be important in a wide number of cell types and diseases. proActiv is an R package that enables the analysis of promoters from RNA-seq data. proActiv uses aligned reads as input, and generates counts and normalized promoter activity estimates for each annotated promoter. In particular, proActiv accepts junction files from TopHat2 or STAR or BAM files as inputs. These estimates can then be used to identify which promoter is active, which promoter is inactive, and which promoters change their activity across conditions. proActiv also allows visualization of promoter activity across conditions.

r-pd-mapping250k-sty 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.mapping250k.sty
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for Affymetrix Mapping250K_Sty
Description:

Platform Design Info for Affymetrix Mapping250K_Sty.

r-pd-feinberg-mm8-me-hx1 0.99.3
Propagated dependencies: r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.feinberg.mm8.me.hx1
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for NimbleGen feinberg_mm8_me_hx1
Description:

Platform Design Info for NimbleGen feinberg_mm8_me_hx1.

r-pd-elegene-1-1-st 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.elegene.1.1.st
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for Affymetrix EleGene-1_1-st
Description:

Platform Design Info for Affymetrix EleGene-1_1-st.

r-pd-medgene-1-0-st 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.medgene.1.0.st
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for Affymetrix MedGene-1_0-st
Description:

Platform Design Info for Affymetrix MedGene-1_0-st.

r-pviz 1.44.0
Propagated dependencies: r-iranges@2.44.0 r-gviz@1.54.0 r-genomicranges@1.62.0 r-data-table@1.17.8 r-biovizbase@1.58.0 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/Pviz
Licenses: Artistic License 2.0
Build system: r
Synopsis: Peptide Annotation and Data Visualization using Gviz
Description:

Pviz adapts the Gviz package for protein sequences and data.

r-pd-2006-07-18-mm8-refseq-promoter 0.99.3
Propagated dependencies: r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.2006.07.18.mm8.refseq.promoter
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for NimbleGen 2006-07-18_mm8_refseq_promoter
Description:

Platform Design Info for NimbleGen 2006-07-18_mm8_refseq_promoter.

r-pd-hg-u95a 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.hg.u95a
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for The Manufacturer's Name HG_U95A
Description:

Platform Design Info for The Manufacturer's Name HG_U95A.

r-pd-chigene-1-0-st 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.chigene.1.0.st
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for Affymetrix ChiGene-1_0-st
Description:

Platform Design Info for Affymetrix ChiGene-1_0-st.

r-pram 1.26.0
Propagated dependencies: r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-rsamtools@2.26.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomicalignments@1.46.0 r-data-table@1.17.8 r-biocparallel@1.44.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://github.com/pliu55/pram
Licenses: GPL 3+
Build system: r
Synopsis: Pooling RNA-seq datasets for assembling transcript models
Description:

Publicly available RNA-seq data is routinely used for retrospective analysis to elucidate new biology. Novel transcript discovery enabled by large collections of RNA-seq datasets has emerged as one of such analysis. To increase the power of transcript discovery from large collections of RNA-seq datasets, we developed a new R package named Pooling RNA-seq and Assembling Models (PRAM), which builds transcript models in intergenic regions from pooled RNA-seq datasets. This package includes functions for defining intergenic regions, extracting and pooling related RNA-seq alignments, predicting, selected, and evaluating transcript models.

r-powsc 1.18.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-rcolorbrewer@1.1-3 r-pheatmap@1.0.13 r-mast@1.36.0 r-limma@3.66.0 r-ggplot2@4.0.1 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/POWSC
Licenses: GPL 2
Build system: r
Synopsis: Simulation, power evaluation, and sample size recommendation for single cell RNA-seq
Description:

Determining the sample size for adequate power to detect statistical significance is a crucial step at the design stage for high-throughput experiments. Even though a number of methods and tools are available for sample size calculation for microarray and RNA-seq in the context of differential expression (DE), this topic in the field of single-cell RNA sequencing is understudied. Moreover, the unique data characteristics present in scRNA-seq such as sparsity and heterogeneity increase the challenge. We propose POWSC, a simulation-based method, to provide power evaluation and sample size recommendation for single-cell RNA sequencing DE analysis. POWSC consists of a data simulator that creates realistic expression data, and a power assessor that provides a comprehensive evaluation and visualization of the power and sample size relationship.

r-prebs 1.50.0
Propagated dependencies: r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rpa@1.66.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomicalignments@1.46.0 r-biobase@2.70.0 r-affy@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/prebs
Licenses: Artistic License 2.0
Build system: r
Synopsis: Probe region expression estimation for RNA-seq data for improved microarray comparability
Description:

The prebs package aims at making RNA-sequencing (RNA-seq) data more comparable to microarray data. The comparability is achieved by summarizing sequencing-based expressions of probe regions using a modified version of RMA algorithm. The pipeline takes mapped reads in BAM format as an input and produces either gene expressions or original microarray probe set expressions as an output.

r-pasillatranscriptexpr 1.38.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/PasillaTranscriptExpr
Licenses: GPL 3+
Build system: r
Synopsis: Data package with transcript expression obtained with kallisto from pasilla knock-down RNA-Seq data from Brooks et al
Description:

This package provides kallisto workflow and transcript expression of RNA-Seq data from Brooks et al.

r-past 1.26.0
Propagated dependencies: r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-rlang@1.1.6 r-qvalue@2.42.0 r-iterators@1.0.14 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-foreach@1.5.2 r-dplyr@1.1.4 r-doparallel@1.0.17
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://github.com/IGBB/past
Licenses: FSDG-compatible
Build system: r
Synopsis: Pathway Association Study Tool (PAST)
Description:

PAST takes GWAS output and assigns SNPs to genes, uses those genes to find pathways associated with the genes, and plots pathways based on significance. Implements methods for reading GWAS input data, finding genes associated with SNPs, calculating enrichment score and significance of pathways, and plotting pathways.

r-pd-maize 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.maize
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for The Manufacturer's Name Maize
Description:

Platform Design Info for The Manufacturer's Name Maize.

r-pd-mogene-2-1-st 3.14.1
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.mogene.2.1.st
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for Affymetrix MoGene-2_1-st
Description:

Platform Design Info for Affymetrix MoGene-2_1-st.

r-phantasuslite 1.8.0
Propagated dependencies: r-stringr@1.6.0 r-rhdf5client@1.32.0 r-httr@1.4.7 r-data-table@1.17.8 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://github.com/ctlab/phantasusLite/
Licenses: Expat
Build system: r
Synopsis: Loading and annotation RNA-seq counts matrices
Description:

PhantasusLite – a lightweight package with helper functions of general interest extracted from phantasus package. In parituclar it simplifies working with public RNA-seq datasets from GEO by providing access to the remote HSDS repository with the precomputed gene counts from ARCHS4 and DEE2 projects.

r-prebsdata 1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/prebsdata
Licenses: Artistic License 2.0
Build system: r
Synopsis: Data for 'prebs' package
Description:

This package contains data required to run examples in prebs package. The data files include: 1) Small sample bam files for demonstration purposes 2) Probe sequence mappings for Custom CDF (taken from http://brainarray.mbni.med.umich.edu/brainarray/Database/CustomCDF/genomic_curated_CDF.asp) 3) Probe sequence mappings for manufacturer's CDF (manually created using bowtie).

r-pd-celegans 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.celegans
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for The Manufacturer's Name Celegans
Description:

Platform Design Info for The Manufacturer's Name Celegans.

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Total results: 68658