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https://www.ravensoundsoftware.com/software/raven-pro/

Software for the acquisition, visualization, measurement, and analysis of sounds. Developed by the Cornell Lab of Ornithology, it is widely used for bioacoustics, allowing researchers to study animal vocalizations and other acoustic signals using spectrograms and waveforms.

Proper citation: RavenPro (RRID:SCR_028144) Copy   

•   Source: SciCrunch Registry

https://www.cdt-africa.org/

World Bank-supported regional center of excellence focused on building capacity for clinical trials, and developing novel vaccines, diagnostics, and therapeutics. Provides training in clinical trials and translational medicine, to foster homegrown health solutions.Training researchers, scientists, and clinical trial staff across Africa in trial management, data management, and scientific writing.

Proper citation: Addis Ababa University Center for Innovative Drug Development and Therapeutic Trials for Africa Core Facility (RRID:SCR_028125) 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://imputation.biodatacatalyst.nhlbi.nih.gov/#!

Free, secure cloud-based service used to impute missing genetic variants in human DNA data, primarily for genome-wide association studies (GWAS). It uses a massive, diverse reference panel of deeply sequenced human genomes to predict missing genotypes, significantly increasing genetic coverage and improving accuracy, particularly for rare variants. It leverages the Trans-Omics for Precision Medicine (TOPMed) panel, which includes over 400 million variants, allowing researchers to boost their genomic data from millions of SNPs to tens of millions.

Proper citation: TOPMed Imputation Server (RRID:SCR_028178) Copy   

•   Source: SciCrunch Registry

https://vitrovivo.com/molecular-histopathology-services/

Specialized biotechnology company that provides histology services, molecular pathology services, and specialized research reagents to accelerate biomedical research. They assist scientists in academia and industry with tissue preparation, immunostaining, 3D cell culture processing, and laser capture microdissection (LCM) for cancer, neuroscience, and drug development studies.

Proper citation: VitroVivo Biotech (RRID:SCR_028175) Copy   

•   Source: SciCrunch Registry

https://grch37.ensembl.org/Homo_sapiens/Tools/LD

Web tool for calculating Linkage Disequilibrium between variants using genotypes from selected population. We only support LD calculation for variants for which we have genotypes from at least 40 samples in the selected population. At the moment we only have sufficient amounts of genotype data from the 1000 Genomes project for human.

Proper citation: Ensembl Linkage Disequilibrium Calculator (RRID:SCR_028177) 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

http://scinetx.com

Local desktop and cloud-based bibliometric and network analysis platform offered through a licensed access model.Supports literature-centered bibliometric and scientometric workflows, and it can also be applied to custom datasets with or without associated literature papers, including broader general network analysis use cases.

Proper citation: SciNetX (RRID:SCR_028186) Copy   

•   Source: SciCrunch Registry

https://github.com/hks5august/CPSM

Software R package that provides comprehensive computational pipeline for predicting survival probabilities and risk groups in cancer patients. Includes dedicated modules to perform key steps such as data preprocessing, training/test splitting, and normalization.

Proper citation: CPSM:Cancer Patient Survival Model (RRID:SCR_028188) Copy   

•   Source: SciCrunch Registry

https://www.tcichemicals.com/

Tokyo Chemical Industry Co., Ltd. (TCI) is a leading global manufacturer of specialty organic chemicals, founded in 1946. They produce over 30,000 research chemicals, including laboratory chemicals, reagents, and functional materials. TCI also acts as a supplier, offering custom synthesis and bulk production from milligrams to tons.

Proper citation: Tokyo Chemical Industry (RRID:SCR_028220) Copy   

•   Source: SciCrunch Registry

https://fr.bimedis.com/vilber-lourmat-fusion-fx7-m503688

Image acquisition system to capture of chemiluminescence and fluorescence images. Using cooled CCD technology in combination with motorised optical lens, Fusion FX7 offers very high sensitivity and extended dynamic range. Data produced are directly compatible with image analysis software developed by VILBER and 1D image can be transformed into 3D results with Bio-1D and the Bio-Gene software.

Proper citation: Vilber Lourmat Fusion FX7 imaging system (RRID:SCR_028219) Copy   

•   Source: SciCrunch Registry

https://www.unza.zm/

Oldest and largest public university established in 1965 in Lusaka. Operating under the motto "Service and Excellence," it offers over 150 undergraduate and postgraduate programs across 13 schools, with major campuses at Great East Road and Ridgeway.

Proper citation: University of Zambia; Lusaka; Zambia (RRID:SCR_028150) Copy   

•   Source: SciCrunch Registry

https://github.com/adamewing/methylartist

Software tools for parsing and plotting methylation patterns. Used for plotting methylation data in various ways.

Proper citation: methylartist (RRID:SCR_028164) 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://github.com/nloyfer/wgbs_tools

Software tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies.

Proper citation: wgbstools (RRID:SCR_028257) 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://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

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://www.nitrc.org/projects/twogrsurvana/

Project to compare two approaches for the construction of longitudinal predictive models, which were used here to estimate the conversion of mild cognitive impairment (MCI) to AD.

Proper citation: Longitudinal survival analysis and two-group comparison for predicting the progression of mild cognitive impairment to Alzheimer (RRID:SCR_028330) 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