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Package Name Access Summary Updated
bioconductor-genomicplot public Plot profiles of next generation sequencing data in genomic features 2024-12-30
r-leapp public These functions take a gene expression value matrix, a primary covariate vector, an additional known covariates matrix. A two stage analysis is applied to counter the effects of latent variables on the rankings of hypotheses. The estimation and adjustment of latent effects are proposed by Sun, Zhang and Owen (2011). "leapp" is developed in the context of microarray experiments, but may be used as a general tool for high throughput data sets where dependence may be involved. 2024-12-30
bioconductor-bionero public Biological Network Reconstruction Omnibus 2024-12-30
bioconductor-rcas public RNA Centric Annotation System 2024-12-30
bioconductor-knowseq public KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline 2024-12-30
r-smartsva public Introduces a fast and efficient Surrogate Variable Analysis algorithm that captures variation of unknown sources (batch effects) for high-dimensional data sets. The algorithm is built on the 'irwsva.build' function of the 'sva' package and proposes a revision on it that achieves an order of magnitude faster running time while trading no accuracy loss in return. 2024-12-30
bioconductor-paa public PAA (Protein Array Analyzer) 2024-12-30
bioconductor-poma public Tools for Omics Data Analysis 2024-12-30
bioconductor-geoexplorer public GEOexplorer: a webserver for gene expression analysis and visualisation 2024-12-30
bioconductor-xde public XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression 2024-12-30
bioconductor-davidtiling public Data and analysis scripts for David, Huber et al. yeast tiling array paper 2024-12-30
bioconductor-spicyr public Spatial analysis of in situ cytometry data 2024-12-30
bioconductor-top public TOP Constructs Transferable Model Across Gene Expression Platforms 2024-12-30
bioconductor-cghmcr public Find chromosome regions showing common gains/losses 2024-12-30
r-tcga2stat public Automatically downloads and processes TCGA genomics and clinical data into a format convenient for statistical analyses in the R environment. 2024-12-30
bioconductor-scbfa public A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq 2024-12-30
bioconductor-rrbsdata public An RRBS data set with 12 samples and 10,000 simulated DMRs 2024-12-30
bioconductor-blma public BLMA: A package for bi-level meta-analysis 2024-12-30
bioconductor-regenrich public Gene regulator enrichment analysis 2024-12-30
bioconductor-svmdo public Identification of Tumor-Discriminating mRNA Signatures via Support Vector Machines Supported by Disease Ontology 2024-12-30
r-easydifferentialgenecoexpression public A function that reads in the GEO code of a list of probesets or gene symbols, a gene expression dataset GEO accession code, the name of the dataset feature discriminating the two conditions for the differential coexpression, and the values of the two different conditions for the differential coexpression, and returns the significant pairs of genes/probesets with highest differential coexpression (p-value < 0.005). If the input gene list is made of gene symbols, this package associates the probesets to these gene symbols, if found. Platforms available: GPL80, 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/>. 2024-12-30
bioconductor-alabaster.spatial public Save and Load Spatial 'Omics Data to/from File 2024-12-30
bioconductor-tradeseq public trajectory-based differential expression analysis for sequencing data 2024-12-30
bioconductor-scrnaseqapp public A single-cell RNAseq Shiny app-package 2024-12-30
bioconductor-feast public FEAture SelcTion (FEAST) for Single-cell clustering 2024-12-30
bioconductor-iseeu public iSEE Universe 2024-12-30
bioconductor-rbec public Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities 2024-12-30
bioconductor-transcriptr public An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification 2024-12-30
bioconductor-soggi public Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals 2024-12-30
bioconductor-factr public Functional Annotation of Custom Transcriptomes 2024-12-30
bioconductor-nullranges public Generation of null ranges via bootstrapping or covariate matching 2024-12-30
bioconductor-plotgardener public Coordinate-Based Genomic Visualization Package for R 2024-12-30
bioconductor-biscuiteer public Convenience Functions for Biscuit 2024-12-30
bioconductor-plyinteractions public Extending tidy verbs to genomic interactions 2024-12-30
bioconductor-chipenrich public Gene Set Enrichment For ChIP-seq Peak Data 2024-12-30
bioconductor-dmrseq public Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing 2024-12-30
bioconductor-methinheritsim public Simulating Whole-Genome Inherited Bisulphite Sequencing Data 2024-12-30
bioconductor-scmeth public Functions to conduct quality control analysis in methylation data 2024-12-30
bioconductor-methylinheritance public Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect 2024-12-30
bioconductor-rjmcmcnucleosomes public Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq) 2024-12-30
bioconductor-bsgenome.drerio.ucsc.danrer11 public Full genome sequences for Danio rerio (UCSC version danRer11) 2024-12-30
bioconductor-bsgenome.hsapiens.ucsc.hg19 public Full genome sequences for Homo sapiens (UCSC version hg19, based on GRCh37.p13) 2024-12-30
bioconductor-redseq public Analysis of high-throughput sequencing data processed by restriction enzyme digestion 2024-12-30
bioconductor-bsgenome.scerevisiae.ucsc.saccer1 public Saccharomyces cerevisiae (Yeast) full genome as provided by UCSC (sacCer1, Oct. 2003) and stored in Biostrings objects. 2024-12-30
bioconductor-bsgenome.btaurus.ucsc.bostau9 public Full genome sequences for Bos taurus (UCSC version bosTau9) 2024-12-30
bioconductor-guideseq public GUIDE-seq and PEtag-seq analysis pipeline 2024-12-30
bioconductor-annotatr public Annotation of Genomic Regions to Genomic Annotations 2024-12-30
bioconductor-chippeakanno public Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data 2024-12-30
bioconductor-methylpipe public Base resolution DNA methylation data analysis 2024-12-30
bioconductor-gothic public Binomial test for Hi-C data analysis 2024-12-30
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