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Package Name Access Summary Updated
bioconductor-scanvis public SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions 2024-12-26
bioconductor-hicvenndiagram public Venn Diagram for genomic interaction data 2024-12-26
bioconductor-ideoviz public Plots data (continuous/discrete) along chromosomal ideogram 2024-12-26
bioconductor-tidycoverage public Extract and aggregate genomic coverage over features of interest 2024-12-26
r-immucellaimouse public ImmuCellAI-mouse is a tool to estimate the abundance of 36 immune cells based on gene expression profile from RNA-Seq or microarray data. 2024-12-26
bioconductor-normr public Normalization and difference calling in ChIP-seq data 2024-12-26
bioconductor-hicaggr public Set of 3D genomic interaction analysis tools 2024-12-26
r-sigqc public Provides gene signature quality control metrics in publication ready plots. Namely, enables the visualization of properties such as expression, variability, correlation, and comparison of methods of standardisation and scoring metrics. 2024-12-26
bioconductor-dmcfb public Differentially Methylated Cytosines via a Bayesian Functional Approach 2024-12-26
bioconductor-epidecoder public epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation 2024-12-26
bioconductor-motifdb public An Annotated Collection of Protein-DNA Binding Sequence Motifs 2024-12-26
bioconductor-scpipe public Pipeline for single cell multi-omic data pre-processing 2024-12-26
bioconductor-coverageview public Coverage visualization package for R 2024-12-26
bioconductor-metagene2 public A package to produce metagene plots 2024-12-26
bioconductor-syntenet public Inference And Analysis Of Synteny Networks 2024-12-26
bioconductor-past public Pathway Association Study Tool (PAST) 2024-12-26
bioconductor-gseabenchmarker public Reproducible GSEA Benchmarking 2024-12-26
r-geneexpressionfromgeo public A function that reads in the GEO code of a gene expression dataset, retrieves its data from GEO, (optionally) retrieves the gene symbols of the dataset, and returns a simple dataframe table containing all the data. Platforms available: GPL11532, GPL23126, GPL6244, GPL8300, GPL80, GPL96, GPL570, GPL571, GPL20115, GPL1293, GPL6102, GPL6104, GPL6883, GPL6884, GPL13497, GPL14550, GPL17077, GPL6480. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>. More information can be found in the following manuscript: Davide Chicco, "geneExpressionFromGEO: an R package to facilitate data reading from Gene Expression Omnibus (GEO)". Microarray Data Analysis, Methods in Molecular Biology, volume 2401, chapter 12, pages 187-194, Springer Protocols, 2021, <doi:10.1007/978-1-0716-1839-4_12>. 2024-12-26
bioconductor-rarr public Read Zarr Files in R 2024-12-26
bioconductor-enrichmentbrowser public Seamless navigation through combined results of set-based and network-based enrichment analysis 2024-12-26
bioconductor-tigre public Transcription factor Inference through Gaussian process Reconstruction of Expression 2024-12-26
bioconductor-gseabase public Gene set enrichment data structures and methods 2024-12-26
bioconductor-preda public Position Related Data Analysis 2024-12-26
bioconductor-globaltest public Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set Testing 2024-12-26
bioconductor-codelink public Manipulation of Codelink microarray data 2024-12-26
bioconductor-mgfm public Marker Gene Finder in Microarray gene expression data 2024-12-26
bioconductor-semdist public Information Accretion-based Function Predictor Evaluation 2024-12-26
bioconductor-idiogram public idiogram 2024-12-26
vamb public Variational autoencoder for metagenomic binning 2024-12-26
bioconductor-ssnappy public Single Sample directioNAl Pathway Perturbation analYsis 2024-12-26
bioconductor-mirnameconverter public Convert miRNA Names to Different miRBase Versions 2024-12-26
bioconductor-ragene10sttranscriptcluster.db public Affymetrix ragene10 annotation data (chip ragene10sttranscriptcluster) 2024-12-26
bioconductor-rgu34c.db public Affymetrix Affymetrix RG_U34C Array annotation data (chip rgu34c) 2024-12-26
bioconductor-raex10stprobeset.db public Affymetrix raex10 annotation data (chip raex10stprobeset) 2024-12-26
bioconductor-ragene10stprobeset.db public Affymetrix ragene10 annotation data (chip ragene10stprobeset) 2024-12-26
bioconductor-ragene20stprobeset.db public Affymetrix ragene20 annotation data (chip ragene20stprobeset) 2024-12-26
bioconductor-ragene21sttranscriptcluster.db public Affymetrix ragene21 annotation data (chip ragene21sttranscriptcluster) 2024-12-26
bioconductor-lumiratall.db public Illumina Rat Illumina expression annotation data (chip lumiRatAll) assembled using data from public repositories 2024-12-26
bioconductor-clariomsrattranscriptcluster.db public Affymetrix clariomsrat annotation data (chip clariomsrattranscriptcluster) 2024-12-26
bioconductor-rwgcod.db public Codelink Rat Whole Genome Bioarray (~34 000 rat gene targets) annotation data (chip rwgcod) assembled using data from public repositories 2024-12-26
bioconductor-rgu34a.db public Affymetrix Affymetrix RG_U34A Array annotation data (chip rgu34a) 2024-12-26
bioconductor-rguatlas4k.db public Clontech BD Atlas Long Oligos Rat 4K annotation data (chip rguatlas4k) assembled using data from public repositories 2024-12-26
bioconductor-rgug4131a.db public Agilent "Rat Genome, Whole" annotation data (chip rgug4131a) assembled using data from public repositories 2024-12-26
bioconductor-rta10probeset.db public Affymetrix rta10 annotation data (chip rta10probeset) 2024-12-26
bioconductor-adme16cod.db public Codelink ADME Rat 16-Assay Bioarray annotation data (chip adme16cod) assembled using data from public repositories 2024-12-26
bioconductor-rgu34b.db public Affymetrix Affymetrix RG_U34B Array annotation data (chip rgu34b) 2024-12-26
bioconductor-ragene11sttranscriptcluster.db public Affymetrix ragene11 annotation data (chip ragene11sttranscriptcluster) 2024-12-26
bioconductor-illuminaratv1.db public Illumina Ratv1 annotation data (chip illuminaRatv1) assembled using data from public repositories 2024-12-26
bioconductor-rae230a.db public Affymetrix Affymetrix RAE230A Array annotation data (chip rae230a) 2024-12-26
bioconductor-rgug4130a.db public Agilent Rat annotation data (chip rgug4130a) assembled using data from public repositories 2024-12-26
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