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http://www.bioconductor.org/packages/release/bioc/html/ropls.html
Software R package for multivariate analysis and feature selection of omics data. Used for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables.
Proper citation: ropls (RRID:SCR_016888) Copy
https://bioconductor.org/packages/release/bioc/html/goseq.html
Software application for performing Gene Ontology analysis on RNAseq data and other length biased data. Used to reduce complexity and highlight biological processes in genome wide expression studies.
Proper citation: Goseq (RRID:SCR_017052) Copy
http://bioconductor.org/packages/GenomicRanges/
Software R package for computing and annotating genomic ranges. Used for storing and manipulating genomic intervals and variables defined along genome.
Proper citation: Genomic Ranges (RRID:SCR_017051) Copy
https://github.com/powellgenomicslab/ascend
Software R package for analysis of single cell RNA-seq expression, normalization and differential expression data. Provides framework to perform cell and gene filtering, quality control, normalization, dimension reduction, clustering, differential expression, and visualization functions.
Proper citation: ascend (RRID:SCR_017257) Copy
Software R package as search tool for single cell RNA-seq data by gene lists. Builds index from scRNA-seq datasets which organizes information in suitable and compact manner so that datasets can be very efficiently searched for either cells or cell types in which given list of genes is expressed.
Proper citation: Scfind (RRID:SCR_017339) Copy
https://bioconductor.org/packages/KEGGgraph/
Software R package interface between KEGG pathway and graph object as well as collection of tools to analyze, dissect and visualize these graphs.
Proper citation: KEGGgraph (RRID:SCR_023788) Copy
http://www.bioconductor.org/packages/release/bioc/html/ReadqPCR.html
A software package that provides functions to read raw RT-qPCR data of different platforms.
Proper citation: ReadqPCR (RRID:SCR_000030) Copy
http://bioconductor.org/packages/release/bioc/html/topGO.html
Software package which provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.
Proper citation: topGO (RRID:SCR_014798) Copy
https://bioconductor.org/packages/release/bioc/html/PhenStat.html
Software R package for statistical analysis of phenotypic data.Tool kit for standardized analysis of high throughput phenotypic data.
Proper citation: PhenStat (RRID:SCR_021317) Copy
https://github.com/PapenfussLab/svaNUMT
Software R package for Nuclear Mitochondrial integration events NUMT detection using structural variant calls.
Proper citation: svaNUMT (RRID:SCR_021381) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/PICS.html
R package with tools that use probabilistic inference of ChIP-Seq. It follows an empirical Bayes mixture model approach.
Proper citation: PICS (RRID:SCR_001093) Copy
https://bioconductor.org/packages/Orthology.eg.db/
Software R package to provide orthology mappings between species, based on NCBI Gene IDs and NCBI orthology mappings.
Proper citation: Orthology.eg.db (RRID:SCR_024740) Copy
https://www.bioconductor.org/packages/release/bioc/html/ExperimentHub.html
Software R package provides central location where curated data from experiments, publications or training courses can be accessed.
Proper citation: ExperimentHub (RRID:SCR_024820) Copy
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