Tools   Select Another Resource Report Type

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

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

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://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://research.utk.edu/oried/core-facilities/advanced-microscopy-and-imaging-center/

Multi-user, multi-disciplinary facility that provides microscopy and imaging services. It houses instrumentation for optical microscopy including laser scanning confocal microscopy and total internal reflection microscopy (TIRF), scanning as well as transmission electron microscopy, MALDI mass spectrometry imaging, and an X-ray MicroCT. Offers complete technical support, individual training and courses that cover both the practical applications and physical principles of microscopy. Provides consultations for development of microscopy projects for inclusion in grant proposals.

Proper citation: University of Tennessee KnoxvilleAdvanced Microscopy and Imaging Center AMIC Core Facility (RRID:SCR_028273) Copy   

•   Source: SciCrunch Registry

https://ycmd.yale.edu/

Full-service core facility specializing in high throughput assay development and screening of chemical and genomic probes.

Proper citation: Yale Center for Molecular Discovery YCMD Core Facility (RRID:SCR_028309) Copy   

•   Source: SciCrunch Registry

https://github.com/andygxzeng/BoneMarrowMap

Software R package to enable rapid reference mapping and annotation of new scRNA-seq data across the spectrum of normal and malignant hematopoietic contexts. Single cell RNA-seq reference map of human hematopoietic development in the bone marrow, with balanced representation of hematopoietic stem and progenitor cells and differentiated populations.

Proper citation: BoneMarrowMap (RRID:SCR_028324) Copy   

•   Source: SciCrunch Registry

https://github.com/maxconway/SNFtool

Software R package for constructing networks of samples (e.g., patients) for each available data type and then efficiently fuses these into one network that represents the full spectrum of underlying data. Used to taking multiple views of a network and merging them into a combined view.

Proper citation: SNFtool (RRID:SCR_028497) Copy   

•   Source: SciCrunch Registry

https://github.com/GangCaoLab/CoolBox

Software Jupyter notebook based genomic data visualization toolkit.

Proper citation: CoolBox (RRID:SCR_028427) 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://github.com/BioinfoUninaScala/MoNETA

Software R package to compress multi-omic data into a single matrix of reduced size. Used for fast and scalable identification of relevant multi-omics relationships between biological entities at the bulk and single-cells level.

Proper citation: MoNETA (RRID:SCR_028485) Copy   

•   Source: SciCrunch Registry

https://github.com/asalavaty/influential

Software R package for identifying and ranking influential nodes in biological and other complex networks. Implements the Integrated Value of Influence (IVI), Experimental data-based Integrative Ranking (ExIR), SIRIR, and numerous network centrality measures, enabling network topology analysis, influential node detection, feature prioritization, and candidate biomarker discovery. Provides functions for network reconstruction, centrality assessment, visualization, and analysis of relationships between centrality measures. Used for identification and classification of the most influential nodes.

Proper citation: influential (RRID:SCR_028517) Copy   

•   Source: SciCrunch Registry

https://uwhistologyandimaging.org/

Core provides histology, immunohistochemistry, imaging, quantitative image analysis, and pathology consultation services. Offers experience, expertise and instrumentation across all platforms. Through the partnership with the Comparative Pathology Program (CPP), we have board certifies veterinary pathologists on staff who are available for research consultation and collaboration.

Proper citation: University of Washington Histology and Imaging Core Facility (RRID:SCR_028435) Copy   

•   Source: SciCrunch Registry

https://bokeh.org/

Software Python package for interactive and static data visualization.Interactive visualization library for modern web browsers. Provides concise construction of graphics and affords high-performance interactivity across large or streaming datasets.

Proper citation: Bokeh (RRID:SCR_028392) 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://gatk.broadinstitute.org/hc/en-us/articles/360036350452-VariantFiltration

Software command-line tool designed for hard-filtering variant callsets (VCF files) by applying user-defined criteria to annotate, rather than remove, low-quality variants. It marks fails in the FILTER field (e.g., using JEXL expressions to filter by DP, QD, or FS), making it essential for filtering small datasets, non-model organisms, or whenever Variant Quality Score Recalibration (VQSR) is not feasible

Proper citation: GATK VariantFiltration (RRID:SCR_028441) Copy   

•   Source: SciCrunch Registry

https://genome.ucsc.edu/goldenpath/help/bigWig.html

Command-line utility provided by the UCSC Genome Browser to convert text-based bedGraph files into indexed binary bigWig files. It is specifically used in bioinformatics to transform dense, continuous genome coverage data into a format that enables fast visualization and remote viewing in genome browsers like IGV or the UCSC Genome Browser.

Proper citation: bedGraphToBigWig (RRID:SCR_028439) Copy   

•   Source: SciCrunch Registry