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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://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
https://www.bioconductor.org/packages/release/bioc/html/sesame.html
Software R package for reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions.
Proper citation: SeSAMe (RRID:SCR_027388) Copy
https://rfxplot.sourceforge.net/
Software toolbox for SPM5 which offers plotting effect sizes, fitted responses, and BOLD time courses averaged across subjects from within 2nd level (random effects) analyses. The toolbox offers a large variety of plot configuration both suitable for data exploration and producing high quality figures for publications.
Proper citation: rfxplot (RRID:SCR_027375) Copy
https://github.com/rnajena/dynamont
Software segmentation/resquiggling tool for ONT signals. Dynamic programming approach to segment ONT signals.
Proper citation: Dynamont (RRID:SCR_027357) Copy
https://brain-bican.github.io/bkbit/
Software package contains tools to use the BICAN Knowledgebase Data Models.
Proper citation: bkbit (RRID:SCR_027564) Copy
https://cran.r-project.org/web/packages/mirt/index.html
Software package for the R Environment. Used for estimating multidimensional item response theory parameters for exploratory and confirmatory models by using maximum-likelihood meth- ods.
Proper citation: mirt (RRID:SCR_027662) Copy
https://cran.r-project.org/web/packages/cmprskcoxmsm/index.html
Software R package uses inverse probability weighting methods to estimate treatment effect under marginal structure model for the cause-specific hazard of competing risk events. Estimates also the cumulative incidence function (i.e. risk) of the potential outcomes, and provides inference on risk difference and risk ratio.
Proper citation: cmprskcoxmsm (RRID:SCR_027665) Copy
https://alleninstitute.github.io/CCF-MAP/descriptions/marmoset_ccf.html
Three-dimensional brain reference atlas based on the RIKEN25v1 MRI-derived template, based on an average of 25 C. jacchus brains resampled to 70 um3 voxel resolution. Includes selected published subcortical parcellations to aid in comparing across parcellation schemes.
Proper citation: HOMBA Adult Marmoset Basal Ganglia Atlas (RRID:SCR_027642) Copy
https://github.com/Core-Bioinformatics/bulkAnalyseR
Software R package for most bulk sequencing datasets. Creates shiny app for interactive data analysis and visualisation. Used for analysing and sharing bulk sequencing results.
Proper citation: bulkAnalyseR (RRID:SCR_027647) Copy
https://www.github.com/bactopia/bactopia
Software pipeline for complete analysis of bacterial genomes.
Proper citation: Bactopia (RRID:SCR_027581) Copy
https://novosparc.readthedocs.io/
Software package for flexible spatial reconstruction of single-cell gene expression with optimal transport. Framework for de novo spatial reconstruction of single-cell gene expression. Assigns cells to tissue locations using probabilistic/optimal-transport models, with or without prior marker information, and returns spatial maps and assignment probabilities.
Proper citation: novoSpaRc (RRID:SCR_027635) Copy
https://alleninstitute.github.io/CCF-MAP/docs/HOMBA_ontology_v1.html
Harmonized cross-species taxonomy of brain and spinal cord structures. Derived from the Allen Developing Human Brain Atlas (DHBA) ontology, the HOMBA is hierarchical, allowing users to aggregate structures from fine grain parcellations to broad regions. Terminology is harmonized across human, primate, and rodent structures with synonymous terms and includes transient developmental structures. HOMBA is designed for neuroanatomical applications including brain sampling and dissection, tissue block mapping, atlas building, cell-type and pathology localization, and linking cross-species and developmental datasets.
Proper citation: Harmonized Ontology of Mammalian Brain Anatomy (HOMBA) (RRID:SCR_027628) Copy
https://cran.r-project.org/web/packages/XYomics/
Software R package for analysis of condition-specific sex differences in omics data. Includes functions for differential expression, interaction testing, and gene regulatory network analysis. Used for analysis of sex differences in omics data for complex diseases.
Proper citation: XYomics (RRID:SCR_027774) Copy
https://cran.r-project.org/package=AER
Software R package contains functions, data sets, examples, demos, and vignettes for the book Christian Kleiber and Achim Zeileis (2008), Applied Econometrics with R, Springer-Verlag, New York. ISBN 978-0-387-77316-2.
Proper citation: AER: Applied Econometrics with R (RRID:SCR_027778) Copy
https://cran.r-project.org/web/packages/ActivePathways/index.html
Software R package for analysing multiple omics datasets in the context of molecular pathways, biological processes and other types of gene sets.Method that first prioritises genes through multi-omics data fusion and then identifies enriched pathways with gene-level evidence from input datasets.
Proper citation: ActivePathways (RRID:SCR_027736) Copy
https://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg38.html
Software R package containing the full genomic sequences for Homo sapiens as provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31).
Proper citation: BSgenome Hsapiens UCSC hg38 (RRID:SCR_027738) Copy
https://github.com/zhoujt1994/scHiCluster
Software Python package for single-cell chromosome contact data analysis. It includes the identification of cell types (clusters), loop calling in cell types, and domain and compartment calling in single cells. Facilitates visualization and comparison of single-cell 3D genomes.
Proper citation: scHiCluster (RRID:SCR_027854) Copy
https://coast.noaa.gov/digitalcoast/tools/btm.html
Software set of tools useful in the analysis of benthic terrain. Includes tools for geomorphology and classification.
Proper citation: Benthic Terrain Modeler (RRID:SCR_027926) Copy
https://github.com/blaserlab/blaseRtools/tree/v0.0.0.9202
Software R tools for Blaser Lab Data Analysis. Package includes commonly used functions for R analysis in the Blaser Lab.
Proper citation: blaseRtools (RRID:SCR_027871) Copy
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