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http://xmedcon.sourceforge.net/

Open source software toolkit for medical image conversion.

Proper citation: XMedCon (RRID:SCR_024366) Copy   

•   Source: SciCrunch Registry

http://www.ks.uiuc.edu/Research/vmd/

Software tool as molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.

Proper citation: VMD (RRID:SCR_024368) Copy   

•   Source: SciCrunch Registry

https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/dna-amplicon.html

Local Run Manager DNA Amplicon analysis module aligns amplicon reads against reference specified in the manifest file. Variants are called for the targeted regions.

Proper citation: DNA Amplicon (RRID:SCR_024481) Copy   

•   Source: SciCrunch Registry

https://github.com/miRTop/mirtop

Command lines tool to annotate miRNAs with standard mirna/isomir naming.

Proper citation: mirtop (RRID:SCR_024116) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/mpsqed/

Software tool for the design of multiplex pyrosequencing assays.

Proper citation: mPSQed (RRID:SCR_024118) Copy   

•   Source: SciCrunch Registry

http://www-igm.univ-mlv.fr/~marsan/smile_english.html

Software tool that infers motifs in set of sequences to infer exceptionnal sites as binding sites in DNA sequences. 1.4 version allows to infer motifs written on any alphabet in any kind of sequences. Allows to deal with motifs associated by some distance constraints. Used to group under unique model different occurrences composed of several boxes separated by spacers of different lengths.

Proper citation: SMILE (RRID:SCR_024119) Copy   

•   Source: SciCrunch Registry

https://www.pkdcure.org/

Organization and funder of polycystic kidney disease research to find treatments. The organization also raises awareness for the disease through education, advocacy and support.

Proper citation: PKD Foundation (RRID:SCR_000209) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/regioneR

Software R package to work with genomic regions. In addition to predefined randomization and evaluation strategies, regioneR is fully customizable. Implements function to evaluate local specificity of detected association. Used for association analysis of genomic regions based on permutation tests.

Proper citation: regioneR (RRID:SCR_028251) Copy   

•   Source: SciCrunch Registry

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

Software package that allows simultaneous analysis of associations between genomic region sets, enabling clustering of data and creation of graphs. Incorporates strategy to improve p-value calculations and normalize z-scores coming from multiple analysis to allow for their direct comparison. Builds upon regioneR by adding new plotting functions for obtaining publication-ready graphs.

Proper citation: regioneReloaded (RRID:SCR_028252) Copy   

•   Source: SciCrunch Registry

https://github.com/ZhuoliHuang/CIMA_BMI_paper

Source analysis and data processing code for article titled "Single-Cell Multi-Omics Insights into BMI-Mediated Immune-Related Disease Risk".

Proper citation: CIMA_BMI_paper (RRID:SCR_028241) Copy   

•   Source: SciCrunch Registry

https://github.com/brentp/somalier

Software application for rapid relatedness estimation for cancer and germline studies using efficient genome sketches extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF. Used for rapid relatedness estimation for cancer and germline studies using efficient genome sketches.

Proper citation: somalier (RRID:SCR_028167) Copy   

•   Source: SciCrunch Registry

https://github.com/nanoporetech/pod5-file-format

File format for storing nanopore DNA data in an easily accessible way. High performance file format for nanopore reads.

Proper citation: pod5 (RRID:SCR_028166) Copy   

•   Source: SciCrunch Registry

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

Software R package provides some legacy utility functions for performing single-cell analyses. Most of these functions are deprecated in favor of newer, more performant alternatives. We just keep this package around for back-compatibility and to point to the replacement functions.

Proper citation: scuttle (RRID:SCR_028419) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/data/experiment/html/scRNAseq.html

Software R package for collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata.

Proper citation: scRNAseq (RRID:SCR_028417) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//release/data/experiment/html/TabulaMurisData.html

Software R package for access to processed 10x (droplet) and SmartSeq2 (on FACS-sorted cells) single-cell RNA-seq data from the Tabula Muris consortium.

Proper citation: TabulaMurisData (RRID:SCR_028418) Copy   

•   Source: SciCrunch Registry

https://doi.org/10.32614/CRAN.package.pairwiseCI

Software R package provides wrapper functions to compute parametric, nonparametric, and bootstrap confidence intervals (CIs) for comparing two samples, specifically designed for all-pairs or many-to-one comparisons. It enables, but does not enforce, adjustments for multiple testing.

Proper citation: pairwiseCI (RRID:SCR_028345) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/lf_patches/

Software MATLAB toolbox for the automatic segmentation of the hippocampus in brain MRI images. It implements a novel patch-based label fusion method that cooperates with a non-rigid registration-based label fusion approach. Used to automatically and accurately segment the hippocampus in MRI scans by combining two techniques.

Proper citation: Combining a patch-based approach with a non-rigid registration-based label fusion method for the hippocampal segmentation (RRID:SCR_028349) Copy   

•   Source: SciCrunch Registry

https://mdv.ndm.ox.ac.uk/docs/documentation/using-chatmdv

Software tool as natural language interface integrated with MDV that allows users to generate high-quality interactive visualisations through natural language commands. ChatMDV employs a retrieval-augmented generation (RAG) pipeline combined with large language models (LLMs) to translate user queries into reproducible Python code and interactive output. Module to add chatbot functionality to query Multi-Dimensional Viewer projects.

Proper citation: ChatMDV (RRID:SCR_028342) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/readr/index.html

Software R package read flat files (csv, tsv, fwf) into R. Used to read rectangular data like 'csv', 'tsv', and 'fwf'. Designed to flexibly parse many types of data found in the wild, while still cleanly failing when data unexpectedly changes.

Proper citation: readr (RRID:SCR_028451) Copy   

•   Source: SciCrunch Registry

https://lume.tv/PANGEA/

Spacial neuron gene expression atlas. Interactive, server-free web application and spatial transcriptomics database designed to help researchers map and analyze gene expression within the brain. Mouse whole brain spatial transcriptomic atlas.

Proper citation: PANGEA (RRID:SCR_028559) Copy   

•   Source: SciCrunch Registry