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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   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/DESeq2.html

Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.

Proper citation: DESeq2 (RRID:SCR_015687) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/AUCell/

Software R package to identify cells with active gene sets in single cell RNA-seq data. Used for analysis of gene set activity in single cell RNA-seq data.Used to calculate whether critical subset of input gene set is enriched within expressed genes for each cell.

Proper citation: AUCell (RRID:SCR_021327) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://scfind.sanger.ac.uk/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://crcview.hegroup.org/

Web-based microarray data analysis and visualization system powered by CRC, or Chinese Restaurant cluster, a Dirichlet process model-based clustering algorithm recently developed by Dr. Steve Qin. It also incorporates several gene expression analysis programs from Bioconductor, including GOStats, genefilter, and Heatplus. CRCView also installs from the Bioconductor system 78 annotation libraries of microarray chips for human (31), mouse (24), rat (14), zebrafish (1), chicken (1), Drosophila (3), Arabidopsis (2), Caenorhabditis elegans (1), and Xenopus Laevis (1). CRCView allows flexible input data format, automated model-based CRC clustering analysis, rich graphical illustration, and integrated Gene Ontology (GO)-based gene enrichment for efficient annotation and interpretation of clustering results. CRC has the following features comparing to other clustering tools: 1) able to infer number of clusters, 2) able to cluster genes displaying time-shifted and/or inverted correlations, 3) able to tolerate missing genotype data and 4) provide confidence measure for clusters generated. You need to register for an account in the system to store your data and analyses. The data and results can be visited again anytime you log in.

Proper citation: CRCView (RRID:SCR_007092) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/epialleleR/

Software R package for calling hypermethylated variant epiallele frequencies at level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map files as input. Used for sensitive allele specific methylation analysis in next generation sequencing data. Used for sensitive detection, quantification and visualisation of mosaic epimutations in methylation sequencing data.

Proper citation: epialleleR (RRID:SCR_023913) Copy   

•   Source: SciCrunch Registry