Tools   Select Another Resource Report Type

https://github.com/vanallenlab/MutPanningV2

Software tool designed to detect rare cancer driver genes from aggregated whole-exome sequencing data.

Proper citation: MutPanningV2 (RRID:SCR_027729) Copy   

•   Source: SciCrunch Registry

https://github.com/sheenamt/msings

Software tool for detecting microsatellite instability by next-generation sequencing.

Proper citation: mSings (RRID:SCR_027728) Copy   

•   Source: SciCrunch Registry

https://www.nbdc-datahub.org

Data platform providing centralized and secure access to rich, longitudinal brain, behavioral, and genomic data from both the Adolescent Brain Cognitive Development (ABCD) and the HEALthy Brain and Child Development (HBCD) Studies. By bringing together data from both studies, the NBDC Data Hub facilitates integrative research on early life and adolescent development, helping researchers explore developmental trajectories across the lifespan.

Proper citation: NIH Brain Development Cohorts (NBDC) Data Hub (RRID:SCR_027710) Copy   

•   Source: SciCrunch Registry

https://liana-py.readthedocs.io/en/latest/

Software framework that adapts and extends existing methods and knowledge to study cell-cell communication in single-cell, spatially-resolved, and multi-modal omics data. All-in-one framework for cell-cell communication inference.

Proper citation: LIANA+ (RRID:SCR_027830) Copy   

•   Source: SciCrunch Registry

https://github.com/HarmonizedMRI/Functional

Software application for vendor-neutral, open-source acquisition and reconstruction protocols for fully harmonized multi-site functional MRI studies.

Proper citation: Functional (RRID:SCR_027832) Copy   

•   Source: SciCrunch Registry

https://www.digitalpsych.org/mindlamp1.html

Core collects data to capture and consider the real-time lived experiences of patients. Uses open-source digital platform and mobile app for neuropsychiatric research and clinical care, to monitor, support, and improve brain health by collecting real-time data (like location, activity, heart rate via sensors), conducting digital assessments (surveys, cognitive tests), and delivering interventions (meditation, journaling, psychoeducation) to patients and clinicians. It helps study behavioral patterns, track symptoms, and personalize mental health treatment through features organized around Learn, Assess, Manage, and Prevent.

Proper citation: BIDMC Division of Digital Psychiatry LAMP platform Core Facility (RRID:SCR_027767) Copy   

•   Source: SciCrunch Registry

http://bionlp.bcgsc.ca/cancermine/

Text-mined and routinely updated database of drivers, oncogenes and tumor suppressors in different types of cancer.

Proper citation: CancerMine (RRID:SCR_027748) Copy   

•   Source: SciCrunch Registry

https://github.com/Illumina/canvas

Software tool for calling copy number variants (CNVs) from human DNA sequencing data. It can work either with germline data, or paired tumor/normal samples. Its primary input is aligned reads (in .bam format), and its primary output is a report (in a .vcf file) giving the copy number status of the genome.

Proper citation: Canvas Copy Number Variant Caller (RRID:SCR_027970) Copy   

•   Source: SciCrunch Registry

https://github.com/schwartzlab-methods/CellNEST

Software tool to decipher patterns of communication. Used to relay-network communication detection that identifies putative ligand–receptor–ligand–receptor communication. Detects T cell homing signals in human lymph nodes, identifies aggressive cancer communication in lung adenocarcinoma and colorectal cancer, and predicts new patterns of communication that may act as relay networks in pancreatic cancer.

Proper citation: CellNEST (RRID:SCR_027883) Copy   

•   Source: SciCrunch Registry

https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction

Software tool for cell type specific enhancer-gene predictions using ABC model.

Proper citation: ABC-Enhancer-Gene-Prediction (RRID:SCR_027918) Copy   

•   Source: SciCrunch Registry

https://github.com/ay-lab/fithic

Software tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.

Proper citation: Fit-Hi-C (RRID:SCR_027917) Copy   

•   Source: SciCrunch Registry

https://camera.niehs.nih.gov/

Interactive database and user interface providing online access to validated alternative methods for U.S. regulatory and other contexts of use. Central hub and unified resource of validated alternative methods that enhances accessibility to validation study reports, data, protocols / SOPs, and information on regulatory guidance.Users can filter searches by alternative method types, defined approaches, Test Method Endpoint, and regulatory guidance.

Proper citation: Collection of Alternative Methods for Regulatory Application (CAMERA) (RRID:SCR_027893) Copy   

•   Source: SciCrunch Registry

http://obsproject.com

Software used for live streaming and high-quality screen recording on Windows, Mac, and Linux. Allows to capture, mix, and arrange multiple audio/video sources—such as webcams, desktop screens, and games—in real-time to create, broadcast, or record customized video content. Cross-platform screencasting and live streaming software application.

Proper citation: OBS Studio (RRID:SCR_028179) Copy   

•   Source: SciCrunch Registry

https://github.com/HuiyangYu/PanDepth

Software tool for calculating sequence depth.

Proper citation: PanDepth (RRID:SCR_028256) Copy   

•   Source: SciCrunch Registry

http://ccb.jhu.edu/software/fqtrim/

Software tool for filtering and trimming next generation sequencing reads.

Proper citation: fqtrim (RRID:SCR_028291) Copy   

•   Source: SciCrunch Registry

http://iregulon.aertslab.org/

Software tool to reverse-engineer transcriptional regulatory networks from co-expressed gene sets by identifying master transcription factors (TFs) and their direct target genes. It operates by scanning for enriched TF binding motifs in promoter regions, utilizing over 10,000 position weight matrices (PWMs) for human, mouse, and Drosophila. Used to enable gene regulatory network mapping directly based on motif enrichment in co-expressed gene set.

Proper citation: iRegulon (RRID:SCR_028223) Copy   

•   Source: SciCrunch Registry

https://oncodb.org/

Database offers integrated multi-omic data for patients across 33 cancer types. It encompasses gene expression, DNA methylation, somatic mutations, proteomic profiles, and chromatin accessibility, drawing from TCGA, GTEx, and CPTAC projects. Users can compare gene expression, DNA methylation, and protein levels between tumor and normal tissues, identifying differentially expressed genes and proteins, and examining gene-to-gene correlations. Provides oncogene mutation profiles and allows for survival analysis based on gene expression and methylation, linked to clinical parameters. Facilitates exploration of multi-omic correlations, such as gene expression with DNA methylation, and their variations with mutation status. Extends its analytical capabilities to include six major oncoviruses, offering insights into their impact on gene expression, methylation, and patient survival.

Proper citation: OncoDB (RRID:SCR_028340) Copy   

•   Source: SciCrunch Registry

https://github.com/bioFAM/MOFA2

Software statistical framework for comprehensive integration of multi-modal single-cell data. Used for integration of multi-omic data sets in unsupervised fashion.

Proper citation: MOFA2 (RRID:SCR_028488) Copy   

•   Source: SciCrunch Registry

https://glycoshape.org/

Database of glycans 3D structural data and information that can be downloaded or used with Re-Glyco to rebuild glycoproteins from the RCSB PDB or EMBL-EBI AlphaFold repositories. Glycan structure database and toolbox designed to restore glycoproteins to their native and functional form.

Proper citation: GlycoShape (RRID:SCR_028443) Copy   

•   Source: SciCrunch Registry

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

Software tool to infer and map cell-to-cell communication networks using single-cell RNA sequencing (scRNA-seq) or proteomics data. Used for inference of intercellular networks from single-cell transcriptomics.

Proper citation: SingleCellSignalR (RRID:SCR_028633) Copy   

•   Source: SciCrunch Registry