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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/higlass/higlass
Web-based visual exploration and analysis of genome interaction maps.
Proper citation: HiGlass (RRID:SCR_026687) Copy
https://github.com/tabatsky/projectionpursuit
Software tool for automated projection pursuit clustering. Alternative clustering approach that alleviates the curse of dimensionality by sequentially projecting high-dimensional data into a low-dimensional representation.
Proper citation: Automated Projection Pursuit (RRID:SCR_026560) Copy
https://bioconductor.org/packages/rrvgo/
Software R package to reduce and visualize Gene Ontology terms. Used for interpreting lists of Gene Ontology terms.
Proper citation: rrvgo (RRID:SCR_026680) Copy
https://github.com/sridevi96/NeuroDevTime
Software code for age prediction in fetal brain and organoid single cell data. This repository contains cell type agnostic models to predict the developmental age of brain cell types from single cell RNAseq data. Code contains 4 jupyter notebooks, which apply pretrained models to predict neurodevelopmental age of cell types in new human fetal brain and organoid datasets.
Proper citation: NeuroDevTime (RRID:SCR_026651) Copy
https://github.com/Neural-Systems-at-UIO/WebWarp
Web application for nonlinear refinement of image registration after WebAlign.
Proper citation: WebWarp (RRID:SCR_026759) Copy
https://github.com/Neural-Systems-at-UIO/WebAlign
Web application for 2D image registration to 3D atlas. Used for user guided affine spatial registration (anchoring) of sectional image data, typically high resolution histological images, to 3D reference atlas space. Can generate user defined cut planes through atlas templates that match orientation of cutting plane of 2D experimental images (atlas maps).
Proper citation: WebAlign (RRID:SCR_026758) Copy
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://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://github.com/BostonGene/Cell_Atlas_MxIF
Software package contains all original code used to process MxIF data.
Proper citation: Cell Atlas MxIF (RRID:SCR_026872) 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://jnm.snmjournals.org/content/46/6/1023.long
Software to evaluate mean absorbed doses to organs and tumors in radionuclide images, providing simple and fast solution for radionuclide imaging and treatment of new drugs in clinical trials. Calculates radiation doses to organs and the whole body based on established human body models.
Proper citation: OLINDA/EXM (RRID:SCR_026835) Copy
https://bitbucket.org/tguenther/read/src/master/
Software tool to infer family relationships for degraded samples. Used to infer degree of relationship (up to second degree, i.e. nephew/niece-uncle/aunt, grandparent-grandchild or half-siblings) for pair of low-coverage individuals.
Proper citation: READ (RRID:SCR_026958) Copy
https://www.dotmatics.com/capabilities/electronic-lab-notebook
Software for scientific research and development. ELN captures and manages experimental data, while Data Discovery Platform enables users to explore, analyze, and visualize that data to gain insights.
Proper citation: Dotmatics ELN and Data Discovery Platform (RRID:SCR_027029) 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://github.com/mskilab-org/JaBbA
Software tool to infer junction-balanced genome graphs with high fidelity. Builds genome graph based on junctions and read depth from whole genome sequencing, inferring optimal copy numbers for both vertices (DNA segments) and edges (bonds between segments).
Proper citation: JaBba (RRID:SCR_027134) Copy
https://bitbucket.org/anthakki/prism/src/master/
Software statistical framework that allows simultaneous extraction of tumor sample composition and cell type and sample specific whole-transcriptome profiles from individual bulk RNA-seq samples.
Proper citation: PRISM - Poisson RNA-profile Identification in Scaled Mixtures (RRID:SCR_027136) Copy
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