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http://www.bioconductor.org/packages/release/bioc/html/qvalue.html

R package that takes a list of p-values resulting from the simultaneous testing of hypotheses and estimates their q-values. It is designed to measure the proportion of false positives when a test is significant. The software is capable of generating plots for visualization. It can be applied to problems in genomics, brain imaging, astrophysics, and data mining.

Proper citation: Qvalue (RRID:SCR_001073) Copy   

•   Source: SciCrunch Registry

https://github.com/howisonlab/softcite-dataset

Gold standard dataset of software mentions in research publications. Provides dataset of annotated software mentions from full text academic literature in biomedicine and economics directly converted from published PDFs with reproducible infrastructure. Includes provenance, and is formatted for immediately usefulness in NLP. Useful for supervised learning at scale.

Proper citation: SoftCite (RRID:SCR_024411) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/HTqPCR.html

Software package for the analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays or OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad Laboratories; conventional 96- or 384-well plates; or microfluidic devices such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features (e.g. genes, microRNAs).

Proper citation: HTqPCR (RRID:SCR_003375) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/microbiome/

Software R package for use in microbiome analysis. Used to provide comprehensive collection of tools and tutorials, with particular focus on amplicon sequencing data.

Proper citation: microbiome (RRID:SCR_024699) Copy   

•   Source: SciCrunch Registry

https://github.com/mikelove/tximport

Software R package for importing pseudoaligned reads into R for use with downstream differential expression analysis. Used for import and summarize transcript level estimates for transcript and gene level analysis.

Proper citation: tximport (RRID:SCR_016752) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/bioc/html/MetaNeighbor.html

Software package to assess cell type identity using both functional and random gene sets. Used for single cell replicability analysis to quantify cell type replicability across datasets using neighbor voting.

Proper citation: MetaNeighbor (RRID:SCR_016727) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/RMassBank.html

Workflow software to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.

Proper citation: RMassBank (RRID:SCR_002797) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/variancePartition/

Software R package to quantify and interpret divers of variation in multilevel gene expression experiments.Provides statistical and visualization framework for studying drivers of variation in RNA-seq datasets in many types of high throughput genomic assays including RNA-seq gene-, exon- and isoform-level quantification, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays and epigenomic sequencing assays.

Proper citation: variancePartition (RRID:SCR_019204) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/synergyfinder/

Software R package as efficient implementations for all popular synergy scoring models for drug combinations, including HSA, Loewe, Bliss and ZIP and visualization of synergy scores as either two dimensional or three dimensional interaction surface over dose matrix. Used to calculate and visualize synergy scores for drug combinations.

Proper citation: SynergyFinder (RRID:SCR_019318) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/fgsea/

Software R package for fast preranked gene set enrichment analysis. Allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.

Proper citation: fgsea (RRID:SCR_020938) Copy   

•   Source: SciCrunch Registry

https://sydneybiox.github.io/CiteFuse/

Software R package consisting of suite of tools for doublet detection, modality integration, clustering, differential RNA and protein expression analysis, antibody-derived tag evaluation, ligand-receptor interaction analysis and interactive web-based visualization of CITE-seq data.

Proper citation: CiteFuse (RRID:SCR_019321) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/ggtree/

Software R package for visualization and annotation of phylogenetic trees with their covariates and other tree like structures with their annotation data. Can import evolutionary data from different tree file formats and analysis programs as well as other associated data from experiments so that various sources and types of data can be displayed on tree for comparison and further analyses.

Proper citation: ggtree (RRID:SCR_018560) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/minet/

Open source software R package for inferring large transcriptional networks using mutual information. Implements algorithms for inferring networks such as gene networks from microarray data.

Proper citation: minet (RRID:SCR_018661) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/scTHI/

Software R package to identify active pairs of ligand receptors from single cells in order to study,among others, tumor host interactions. Contains set of signatures to classify cells from tumor microenvironment.

Proper citation: scTHI (RRID:SCR_018918) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/org.Hs.eg.db/

Software R package as object for simple mapping of Entrez Gene identifiers https://www.ncbi.nlm.nih.gov/ entrez/query.fcgi?db=gene to all possible GenBank accession numbers.

Proper citation: org.Hs.eg.db (RRID:SCR_024739) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/combi/

Software R package for simultaneous exploration of multiple datasets. Compositional omics model based visual integration.Used to integrate omics data for visualization, with special focus on compositionality.

Proper citation: combi (RRID:SCR_024986) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/org.Rn.eg.db/

Software R tool for genome wide annotation for Rat, primarily based on mapping using Entrez Gene identifiers.

Proper citation: org.Rn.eg.db (RRID:SCR_018358) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/ChIPseeker/

Software package to retrieve nearest genes around peak, annotate genomic region of peak, implements statstical methods for estimate significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare own dataset with those deposited in database.Several visualization functions are implemented to summarize coverage of peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.

Proper citation: ChIPseeker (RRID:SCR_021322) Copy   

•   Source: SciCrunch Registry

http://imlspenticton.uzh.ch:3838/CATALYSTLite/

Software tool as interactive Shiny web application that provides user interface to mass cytometry data processing pipeline implemented in CATALYST R Bioconductor package.

Proper citation: CATALYSTLite (RRID:SCR_017126) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/EGSEA/

Method developed for RNA-sequencing data. EGSEA combines results from twelve algorithms and calculates collective gene set scores to improve the biological relevance of the highest ranked gene sets.

Proper citation: EGSEA (RRID:SCR_015036) Copy   

•   Source: SciCrunch Registry