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https://bio.tools/dupradar

Software R package for assessment of PCR artifacts in RNA-Seq data. Used for duplication rate quality control for RNA-Seq datasets.

Proper citation: dupRadar (RRID:SCR_027976) Copy   

•   Source: SciCrunch Registry

https://github.com/AlexanRNA/nanowgs/releases/tag/v0.0.2

Nextflow pipeline to process whole genome long-read sequencing data generated in the context of ASAP project.

Proper citation: NanoWGS (RRID:SCR_028113) Copy   

•   Source: SciCrunch Registry

https://ipfx.readthedocs.io/

Software Python package for computing intrinsic cell features from electrophysiology data. Used to compute intrinsic cell features from intracellular electrophysiology data.

Proper citation: Intrinsic Physiology Feature Extractor (RRID:SCR_028075) Copy   

•   Source: SciCrunch Registry

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

Software R package for reference sequence checksums for provenance identification in RNA-seq. Performs numerous annotation and metadata gathering tasks on behalf of users during the import of transcript counts and abundance from quantification tools such as salmon. Data are imported as SummarizedExperiment objects with associated GenomicRanges metadata. Correct metadata is added automatically via reference sequence digests, facilitating genomic analyses and assisting in computational reproducibility.

Proper citation: tximeta (RRID:SCR_028005) Copy   

•   Source: SciCrunch Registry

https://jokergoo.github.io/rGREAT/

Software R package for functional enrichment on genomic regions. Functional enrichment analysis directly performed on genomic regions.

Proper citation: rGREAT (RRID:SCR_028008) Copy   

•   Source: SciCrunch Registry

https://histoatlas.com

Pan-cancer morphology atlas linking histological features to molecular and clinical outcomes. Structured way to explore cancer morphology at scale and connect tissue organization with patient outcomes and molecular signatures, enabling translational researchers to systematically discover and evaluate pathology-based biomarkers.

Proper citation: HistoAtlas (RRID:SCR_028056) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/compareGroups/

Software R package to create tables displaying results of univariate analyses, stratified or not by categorical variable groupings.

Proper citation: compareGroups (RRID:SCR_027994) 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://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://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

https://bioconductor.posit.co/packages/3.20/data/annotation/html/IlluminaHumanMethylationEPICv2anno.20a1.hg38.html

Software R annotation package for Illumina's EPIC v2.0 methylation arrays. The version 2 covers more than 935K CpG sites in the human genome hg38. It is an update of the original EPIC v1.0 array (i.e., the 850K methylation array).

Proper citation: IlluminaHumanMethylationEPICv2anno (RRID:SCR_028569) Copy   

•   Source: SciCrunch Registry

https://www.scienceverse.org/metacheck/

Software R package to audit research outputs for compliance with open science best practices. Evaluates adherence to standards such as pre-registration and data availability. Used for automated checks of research outputs for best practices.

Proper citation: MetaCheck (RRID:SCR_028666) Copy   

•   Source: SciCrunch Registry

https://mycompounddiscoverer.com/

Software platform by Thermo Fisher Scientific designed for identifying, comparing, and interpreting small molecules in complex biological, environmental, and forensic samples. It uses customizable workflow, known as nodes, to automate mass spectrometry data processing, spectral library searching, and statistical analysis.Compound Discoverer is integrated with SIRIUS (via a custom workflow node) to bridge the gap between high-resolution MS/MS data and confident molecular identification. While Thermo Scientific’s Compound Discoverer excels at library searching and statistical analysis, SIRIUS provides powerful in silico tools to accurately predict molecular formulas, chemical classes, and de novo structures. High-resolution mass spectrometry (HRMS) data analysis software for untargeted metabolomics, lipidomics, and contaminant screening. Utilizes modular workflows to extract features, match spectra against libraries like mzCloud, and confidently identify complex organic compounds.

Proper citation: Compound Discoverer (RRID:SCR_028693) Copy   

•   Source: SciCrunch Registry

https://insitupy.readthedocs.io/en/latest/

Software Python package for analysis of single-cell spatial transcriptomics data. Used to read, visualize, and analyze the spatially resolved gene expression within one dataset but also across different datasets. Provides general structure for organizing multiple datasets and its corresponding metadata.

Proper citation: InSitupy (RRID:SCR_028769) Copy   

•   Source: SciCrunch Registry