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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://github.com/cogent3/cogent3
Software Python library for analysis of genomic sequence data. Framework for novel probabilistic analyses of biological sequences, devising workflows, and generating publication quality graphics.
Proper citation: PyCogent (RRID:SCR_024192) Copy
https://github.com/open2c/cooler
Software library for sparse, compressed, binary persistent storage format used to store genomic interaction data, such as Hi-C contact matrices.Scalable storage for Hi-C data and other genomically labeled arrays.
Proper citation: Cooler (RRID:SCR_024194) Copy
https://bioconductor.org/packages/release/bioc/html/AnnotationHub.html
Software R package to provide a client for the Bioconductor AnnotationHub web resource. AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered.
Proper citation: AnnotationHub (RRID:SCR_024227) Copy
https://bioconductor.org/packages/hypergraph/
Software R package that implements some simple capabilities for representing and manipulating hypergraphs.
Proper citation: hypergraph (RRID:SCR_024240) Copy
https://bioconductor.org/packages/HTSFilter/
Software R package implements filtering procedure for replicated transcriptome sequencing data based on global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions.
Proper citation: htsfilter (RRID:SCR_024242) Copy
https://bioconductor.org/packages/release/bioc/html/MultiAssayExperiment.html
Software R package to harmonize data management of multiple experimental assays performed on overlapping set of specimens.Provides user experience by extending concepts from SummarizedExperiment, supporting open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames. Facilities are provided for reshaping data into wide and long formats for adaptability to graphing and downstream analysis.
Proper citation: multiassayexperiment (RRID:SCR_024245) Copy
https://bioconductor.org/packages/release/bioc/html/MutationalPatterns.html
Software R package provides set of flexible functions to evaluate and visualize multitude of mutational patterns in base substitution catalogues of e.g. healthy samples, tumour samples, or DNA-repair deficient cells.
Proper citation: mutationalpatterns (RRID:SCR_024247) Copy
https://bioconductor.org/packages/groHMM/
Software R package for analysis of GRO-seq data. Used for identifying unannotated and cell type-specific transcription units from global run-on sequencing data
Proper citation: groHMM (RRID:SCR_024237) Copy
https://bioconductor.org/packages/genefilter/
Software R package provides some basic functions for filtering genes.
Proper citation: genefilter (RRID:SCR_024238) Copy
https://cran.r-project.org/package=RANN
Software R package finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library (v1.1.3).
Proper citation: rann (RRID:SCR_024297) Copy
https://github.com/denglab/SeqSero
Software pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies.
Proper citation: seqsero (RRID:SCR_024333) Copy
https://cran.r-project.org/package=RNeXML
Software R package provides access to phyloinformatic data in 'NeXML' format.
Proper citation: rnexml (RRID:SCR_024291) Copy
https://cran.r-project.org/package=phylobase
Software R package provides base S4 class for comparative methods, incorporating one or more trees and trait data. Used for phylogenetic analysis.
Proper citation: phylobase (RRID:SCR_024292) Copy
https://cran.r-project.org/web/packages/qqman/index.html
Software R package to create Q-Q and manhattan plots for GWAS data from PLINK output files.
Proper citation: qqman (RRID:SCR_024293) Copy
https://synonym.caltech.edu/software/sbmltoolbox/
Software toolbox provides set of basic functions allowing SBML models to be used in both MATLAB and Octave.
Proper citation: sbmltoolbox (RRID:SCR_024329) Copy
https://cran.r-project.org/package=tigger
Software R package infers V genotype of individual from immunoglobulin repertoire sequencing data like AIRR-Seq, Rep-Seq. Includes detection of any novel alleles. This information is then used to correct existing V allele calls from among sample sequences.
Proper citation: tigger (RRID:SCR_024310) Copy
https://cran.r-project.org/package=wavethresh
Software R package to perform 1, 2 and 3D real and complex-valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage for various kinds of data, locally stationary wavelet time series, nonstationary multiscale transfer function modeling, density estimation.
Proper citation: wavethresh (RRID:SCR_024311) Copy
https://cran.r-project.org/package=WebGestaltR
Software R package to support gene set enrichment analysis, network topology analysis.Can be integrated into other pipeline or simultaneously analyze multiple gene lists. The user-friendly output report allows interactive and efficient exploration of enrichment results.
Proper citation: webgestaltr (RRID:SCR_024312) Copy
https://cran.r-project.org/web/packages/sjPlot/index.html
Software R package as collection of plotting and table output functions for data visualization. Results of various statistical analyses that are commonly used in social sciences can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, generalized linear models, mixed effects models, principal component analysis and correlation matrices, cluster analyses, scatter plots, stacked scales, effects plots of regression models including interaction terms. This package supports labelled data.
Proper citation: sjplot (RRID:SCR_024307) Copy
https://cran.r-project.org/package=waveslim
Software R package for basic wavelet routines for time series 1D, image 2D and array 3D analysis.
Proper citation: waveslim (RRID:SCR_024308) Copy
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