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Package Name Access Summary Updated
bioconductor-wiggleplotr public Make read coverage plots from BigWig files 2024-12-26
bioconductor-plyranges public A fluent interface for manipulating GenomicRanges 2024-12-26
bioconductor-dmchmm public Differentially Methylated CpG using Hidden Markov Model 2024-12-26
bioconductor-chipenrich.data public Companion package to chipenrich 2024-12-26
r-easylift public A convenience package for converting between popular mouse & human builds. 2024-12-26
bioconductor-roar public Identify differential APA usage from RNA-seq alignments 2024-12-26
bioconductor-seqsetvis public Set Based Visualizations for Next-Gen Sequencing Data 2024-12-26
bioconductor-hitc public High Throughput Chromosome Conformation Capture analysis 2024-12-26
bioconductor-consensusseeker public Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges 2024-12-26
bioconductor-rifi public 'rifi' analyses data from rifampicin time series created by microarray or RNAseq 2024-12-26
bioconductor-r3cseq public Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq) 2024-12-26
bioconductor-chromheatmap public Heat map plotting by genome coordinate 2024-12-26
bioconductor-excluster public ExCluster robustly detects differentially expressed exons between two conditions of RNA-seq data, requiring at least two independent biological replicates per condition 2024-12-26
bioconductor-rificomparative public 'rifiComparative' compares the output of rifi from two different conditions. 2024-12-26
bioconductor-pram public Pooling RNA-seq datasets for assembling transcript models 2024-12-26
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
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