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http://www.bioconductor.org/packages/2.12/bioc/html/Rolexa.html
Software that provides probabilistic base calling, quality checks and diagnostic plots for Solexa sequencing data.
Proper citation: Rolexa (RRID:SCR_013017) Copy
http://bioconductor.org/packages/2.12/bioc/html/cn.mops.html
A data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data.
Proper citation: cn.mops (RRID:SCR_013036) Copy
http://www.bioconductor.org/packages//2.10/bioc/html/HiTC.html
Software package to explore high-throughput ''C'' data such as 5C or Hi-C.
Proper citation: HiTC (RRID:SCR_013175) Copy
http://www.bioconductor.org/packages/2.9/bioc/html/Repitools.html
Software tools for the analysis of enrichment-based epigenomic data.
Proper citation: Repitools (RRID:SCR_013242) Copy
http://www.bioconductor.org/packages//2.10/bioc/html/CancerMutationAnalysis.html
Software package that implements gene and gene-set level analysis methods for somatic mutation studies of cancer.
Proper citation: CancerMutationAnalysis (RRID:SCR_013181) Copy
http://www.bioconductor.org/packages/release/bioc/html/SRAdb.html
Software package to make access to the compilation of metadata from NCBI SRA and tools associated with submission, study, sample, experiment and run much more feasible. This is accomplished by parsing all the NCBI SRA metadata into a SQLite database that can be stored and queried locally. Fulltext search in the package make querying metadata very flexible and powerful. fastq and sra files can be downloaded for doing alignment locally. Beside ftp protocol, the SRAdb has funcitons supporting fastp protocol (ascp from Aspera Connect) for faster downloading large data files over long distance. The SQLite database is updated regularly as new data is added to SRA and can be downloaded at will for the most up-to-date metadata.
Proper citation: SRAdb (RRID:SCR_006524) Copy
http://www.bioconductor.org/packages/release/bioc/html/MethylSeekR.html
A software package for the discovery of regulatory regions from Bis-seq data.
Proper citation: MethylSeekR (RRID:SCR_006513) Copy
http://bioconductor.org/packages/release/bioc/html/casper.html
Software to infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision.
Proper citation: casper (RRID:SCR_006613) Copy
http://www.bioconductor.org/packages/devel/bioc/html/ChIPXpress.html
A R package designed to improve ChIP-seq and ChIP-chip target gene ranking using publicly available gene expression data. It takes as input predicted transcription factor (TF) bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target.
Proper citation: ChIPXpress (RRID:SCR_006653) Copy
http://watson.nci.nih.gov/bioc_mirror/packages/2.11/bioc/html/EDASeq.html
Software for numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: EDASeq (RRID:SCR_006751) Copy
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
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
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
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
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
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
http://bioconductor.org/packages/gage/
Software R package for gene set enrichment or pathway analysis. Applicable independent of microarray or RNAseq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity. Pipeline routines of multiple GAGE analyses in batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources and studies.
Proper citation: GAGE (RRID:SCR_017067) Copy
http://bioconductor.org/packages/release/data/experiment/html/affydata.html
Software R package for analysis of Affymetrix Data. Contains samples data files of a large size.
Proper citation: affydata (RRID:SCR_016976) Copy
http://bioconductor.org/packages/CATALYST/
Software R package to provide pipeline for preprocessing of cytometry data, including normalization using bead standards, single cell deconvolution, and bead based compensation.
Proper citation: CATALYST (RRID:SCR_017127) Copy
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
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