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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
https://www.bioconductor.org/packages/release/bioc/html/GSVA.html
Open source software R package for assaying variation of gene set enrichment over sample population.Used for microarray and RNA-seq data analysis. Gene set enrichment method that estimates variation of pathway activity over sample population in unsupervised manner.
Proper citation: GSVA (RRID:SCR_021058) Copy
https://bioconductor.org/packages/SimFFPE/
Software R package to simulate artifact chimeric reads specifically generated in next generation sequencing process of formalin fixed paraffin embedded tissue. Simulates normal reads as well as artifact chimeric reads that are enriched in FFPE samples. These artifact chimeric reads can lead to large amounts of false positive structural variant calls.
Proper citation: SimFFPE (RRID:SCR_021085) Copy
https://bioconductor.org/packages/EGAD/
Software package implements series of highly efficient tools to calculate functional properties of networks based on guilt by association methods. Ultra fast functional analysis of gene networks.
Proper citation: Extending Guilt by Association by Degree (RRID:SCR_018427) Copy
https://bioconductor.org/packages/StructuralVariantAnnotation/
Software R package for structural variant analysis. Contains helper functions for dealing with structural variants in VCF format. Contains functions for parsing VCFs from number of popular callers as well as functions for dealing with breakpoints involving two separate genomic loci encoded as GRanges objects.
Proper citation: StructuralVariantAnnotation (RRID:SCR_018683) Copy
https://www.ncbi.nlm.nih.gov/geo/info/geo2r.html
Software as an interactive web tool to compare two or more groups of samples in a Gene Expression Omnibus (GEO) series regardless of data type and quality. Used to identify genes that are differentially expressed across experimental conditions. Results are presented as a table of genes ordered by significance.
Proper citation: GEO2R (RRID:SCR_016569) 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://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/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
http://www.bioconductor.org/packages/release/bioc/html/ncdfFlow.html
Software package that provides netCDF storage based methods and functions for manipulation of flow cytometry data.
Proper citation: ncdfFlow (RRID:SCR_000009) Copy
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