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bioconductor-poma
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public |
Tools for Omics Data Analysis
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2024-12-30 |
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bioconductor-geoexplorer
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public |
GEOexplorer: a webserver for gene expression analysis and visualisation
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2024-12-30 |
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bioconductor-xde
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public |
XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression
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2024-12-30 |
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bioconductor-davidtiling
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public |
Data and analysis scripts for David, Huber et al. yeast tiling array paper
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2024-12-30 |
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bioconductor-spicyr
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public |
Spatial analysis of in situ cytometry data
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2024-12-30 |
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bioconductor-top
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public |
TOP Constructs Transferable Model Across Gene Expression Platforms
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2024-12-30 |
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bioconductor-cghmcr
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public |
Find chromosome regions showing common gains/losses
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2024-12-30 |
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r-tcga2stat
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public |
Automatically downloads and processes TCGA genomics and clinical data into a format convenient for statistical analyses in the R environment.
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2024-12-30 |
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bioconductor-scbfa
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public |
A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq
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2024-12-30 |
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bioconductor-rrbsdata
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public |
An RRBS data set with 12 samples and 10,000 simulated DMRs
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2024-12-30 |
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bioconductor-blma
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public |
BLMA: A package for bi-level meta-analysis
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2024-12-30 |
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bioconductor-regenrich
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public |
Gene regulator enrichment analysis
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2024-12-30 |
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bioconductor-svmdo
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public |
Identification of Tumor-Discriminating mRNA Signatures via Support Vector Machines Supported by Disease Ontology
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2024-12-30 |
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r-easydifferentialgenecoexpression
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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/>.
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2024-12-30 |
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bioconductor-alabaster.spatial
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public |
Save and Load Spatial 'Omics Data to/from File
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2024-12-30 |
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bioconductor-tradeseq
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public |
trajectory-based differential expression analysis for sequencing data
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2024-12-30 |
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bioconductor-scrnaseqapp
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public |
A single-cell RNAseq Shiny app-package
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2024-12-30 |
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bioconductor-feast
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public |
FEAture SelcTion (FEAST) for Single-cell clustering
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2024-12-30 |
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bioconductor-iseeu
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public |
iSEE Universe
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2024-12-30 |
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bioconductor-rbec
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public |
Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities
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2024-12-30 |
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bioconductor-transcriptr
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public |
An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification
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2024-12-30 |
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bioconductor-soggi
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public |
Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals
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2024-12-30 |
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bioconductor-factr
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public |
Functional Annotation of Custom Transcriptomes
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2024-12-30 |
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bioconductor-nullranges
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public |
Generation of null ranges via bootstrapping or covariate matching
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2024-12-30 |
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bioconductor-plotgardener
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public |
Coordinate-Based Genomic Visualization Package for R
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2024-12-30 |
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bioconductor-biscuiteer
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public |
Convenience Functions for Biscuit
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2024-12-30 |
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bioconductor-plyinteractions
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public |
Extending tidy verbs to genomic interactions
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2024-12-30 |
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bioconductor-chipenrich
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public |
Gene Set Enrichment For ChIP-seq Peak Data
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2024-12-30 |
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bioconductor-dmrseq
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public |
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
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2024-12-30 |
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bioconductor-methinheritsim
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public |
Simulating Whole-Genome Inherited Bisulphite Sequencing Data
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2024-12-30 |
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bioconductor-scmeth
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public |
Functions to conduct quality control analysis in methylation data
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2024-12-30 |
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bioconductor-methylinheritance
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public |
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect
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2024-12-30 |
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bioconductor-rjmcmcnucleosomes
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public |
Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)
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2024-12-30 |
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bioconductor-bsgenome.drerio.ucsc.danrer11
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public |
Full genome sequences for Danio rerio (UCSC version danRer11)
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2024-12-30 |
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bioconductor-bsgenome.hsapiens.ucsc.hg19
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public |
Full genome sequences for Homo sapiens (UCSC version hg19, based on GRCh37.p13)
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2024-12-30 |
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bioconductor-redseq
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public |
Analysis of high-throughput sequencing data processed by restriction enzyme digestion
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2024-12-30 |
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bioconductor-bsgenome.scerevisiae.ucsc.saccer1
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public |
Saccharomyces cerevisiae (Yeast) full genome as provided by UCSC (sacCer1, Oct. 2003) and stored in Biostrings objects.
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2024-12-30 |
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bioconductor-bsgenome.btaurus.ucsc.bostau9
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public |
Full genome sequences for Bos taurus (UCSC version bosTau9)
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2024-12-30 |
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bioconductor-guideseq
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public |
GUIDE-seq and PEtag-seq analysis pipeline
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2024-12-30 |
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bioconductor-annotatr
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public |
Annotation of Genomic Regions to Genomic Annotations
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2024-12-30 |
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bioconductor-chippeakanno
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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
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2024-12-30 |
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bioconductor-methylpipe
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public |
Base resolution DNA methylation data analysis
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2024-12-30 |
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bioconductor-gothic
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public |
Binomial test for Hi-C data analysis
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2024-12-30 |
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bioconductor-tapseq
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public |
Targeted scRNA-seq primer design for TAP-seq
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2024-12-30 |
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bioconductor-bsgenome.vvinifera.urgi.iggp8x
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public |
Full reference nuclear genome sequences for Vitis vinifera subsp. vinifera PN40024 (derived from Pinot Noir and close to homozygosity after 6-9 rounds of selfing) as assembled by the IGGP (version 8X) and available at the URGI (INRA). More details in Jaillon et al (Nature, 2007).
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2024-12-30 |
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bioconductor-bsgenome.rnorvegicus.ucsc.rn7
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public |
Full genome sequences for Rattus norvegicus (UCSC genome rn7)
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2024-12-30 |
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bioconductor-bsgenome.rnorvegicus.ucsc.rn5
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public |
Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn5, Mar. 2012) and stored in Biostrings objects.
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2024-12-30 |
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bioconductor-genomation
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public |
Summary, annotation and visualization of genomic data
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2024-12-30 |
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bioconductor-bsgenome.btaurus.ucsc.bostau3
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public |
Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau3, Aug. 2006) and stored in Biostrings objects.
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2024-12-30 |
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bioconductor-spiky
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public |
Spike-in calibration for cell-free MeDIP
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2024-12-30 |
