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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://bioconductor.org/packages/csaw/
Software R package for detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.
Proper citation: CSAW (RRID:SCR_026738) Copy
https://github.com/statgen/popscle
Software suite of population scale analysis tools for single-cell genomics data.
Proper citation: popscle (RRID:SCR_026707) Copy
https://CRAN.R-project.org/package=broom.mixed
Software R package for tidying output of statistical models.
Proper citation: broom.mixed (RRID:SCR_026712) Copy
https://www.bioconductor.org/packages/release/bioc/html/singleCellTK.html
Software R package provides interface to popular tools for importing, quality control, analysis, and visualization of single cell RNA-seq data. Allows users to integrate tools from various packages at different stages of analysis workflow.
Proper citation: singleCellTK (RRID:SCR_026813) Copy
https://cran.r-project.org/web/packages/BioVenn/index.html
Software R and Python package for comparison and visualization of biological identifiers lists using area-proportional Venn diagrams. Also offers option to map Entrez and/or Affymetrix IDs to Ensembl IDs. In SVG mode, text and numbers can be dragged and dropped. Used to create area-proportional Venn diagram of 2 or 3 circles.
Proper citation: BioVenn (RRID:SCR_026853) Copy
https://bioconductor.org/packages/release/bioc/html/apeglm.html
Software package provides Bayesian shrinkage estimators for effect sizes for variety of GLM models, using approximation of posterior for individual coefficients.
Proper citation: apeglm (RRID:SCR_026951) Copy
https://github.com/PathoGenOmics-Lab/VIPERA
Software package to automate analysis of evolutionary trajectories over time of series of sequences from same viral infection. Snakemake workflow for SARS-CoV-2 viral intra-patient evolution reporting and analysis.
Proper citation: VIPERA (RRID:SCR_026964) Copy
https://cran.r-project.org/web/packages/CPE/index.html
Software R package used in survival analysis that evaluates predictive accuracy of survival model. Measures how well model can distinguish between pairs of individuals with different survival times. Calculates proportion of all pairs of individuals whose predicted survival times are correctly ordered.
Proper citation: Concordance Probability Estimates (RRID:SCR_027140) Copy
https://cran.r-project.org/web/packages/mvmeta/index.html
Software R package to perform fixed and random-effects multivariate and univariate meta-analysis and meta-regression.
Proper citation: mvmeta (RRID:SCR_027142) Copy
https://cran.r-project.org/web/packages/mediation/index.html
Software R package for estimation of causal mediation effects. Allows researchers to conduct sensitivity analysis for certain parametric models.
Proper citation: mediation (RRID:SCR_026984) Copy
http://www.atgc-montpellier.fr/permutmatrix/
Software package for analysing and visualising data. Graphical environment to arrange gene expression profiles in optimal linear order.
Proper citation: PermutMatrix (RRID:SCR_026979) Copy
https://cran.r-project.org/web/packages/BAMMtools/index.html
Software R package for analysis and visualization of macroevolutionary dynamics on phylogenetic trees.
Proper citation: BAMMtools (RRID:SCR_027137) Copy
https://github.com/gillislab/MetaMarkers
Software R package to efficiently compute robust markers across single-cell datasets. Robust marker signatures from single-cell data.
Proper citation: MetaMarkers (RRID:SCR_027104) Copy
https://caravagnalab.github.io/CNAqc/
Software package to quality control bulk cancer sequencing data. Used to visualise and manipulate i) somatic mutation data of both single-nucleotide variants and insertion-deletions, ii) allele-specific Copy Number Alterations (CNAs) and iii) tumour purity estimates. Used to validate copy number segmentations against variant allele frequencies of somatic mutations. Provides automatic copy number calling pipeline. Provides also algorithms to phase mutation multiplicities against CNAs and estimate Cancer Cell Fractions (CCFs) with their uncertainty.
Proper citation: CNAqc (RRID:SCR_027066) Copy
https://cran.r-project.org/web/packages/babelgene/index.html
Software R package to convert between human and non-human gene orthologs/homologs. Integrates orthology assertion predictions sourced from multiple databases as compiled by the HGNC Comparison of Orthology Predictions (HCOP) (Wright et al. 2005 , Eyre et al. 2007 , Seal et al. 2011 ).
Proper citation: babelgene (RRID:SCR_027117) Copy
https://bioconductor.org/packages/release/bioc/html/UCell.html
Software package for evaluating gene signatures in single-cell datasets. UCell signature scores, based on the Mann-Whitney U statistic, are robust to dataset size and heterogeneity, and their calculation demands less computing time and memory than other available methods, enabling the processing of large datasets in a few minutes even on machines with limited computing power. UCell can be applied to any single-cell data matrix, and includes functions to directly interact with SingleCellExperiment and Seurat objects.
Proper citation: UCell (RRID:SCR_027109) Copy
https://cran.r-project.org/web/packages/flexmix/index.html
Software R package for finite mixtures of regression models using EM algorithm. General framework for finite mixture models and latent class regression in R.
Proper citation: flexmix (RRID:SCR_027152) Copy
https://www.bioconductor.org/packages//2.7/data/annotation/html/hgu133plus2.db.html
Software R package for Affymetrix Human Genome U133 Plus 2.0 Array annotation data.
Proper citation: chip hgu133plus2 (RRID:SCR_027245) Copy
https://gitee.com/zhixingfeng/NanoFreeLunch.jl
Software toolkit for quantitative detection of DNA methylation from nanopore sequencing data without raw signals.
Proper citation: NanoFreeLunch (RRID:SCR_027196) Copy
https://www.bioconductor.org/packages/release/bioc/html/IsoformSwitchAnalyzeR.html
Software R package to identify, annotate and visualize isoform switches with functional consequences from both short- and long-read RNA-seq data. Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.
Proper citation: IsoformSwitchAnalyzeR (RRID:SCR_027320) Copy
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