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Database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice. The database currently holds more than 1000 images of lesions from mutant mice and their inbred backgrounds and further images are being added continuously. Images can be retrieved by searching for specific lesions or class of lesion, by genetic locus, or by a wide set of parameters shown on the Advanced Search Interface. Its two key aims are: * To provide a searchable database of histopathology images derived from experimental manipulation of the mouse genome or experiments conducted on genetically manipulated mice. * A reference / didactic resource covering all aspects of mouse pathology Lesions are described according to the Pathbase pathology ontology developed by the Pathbase European Consortium, and are available at the site or on the Gene Ontology Consortium site - OBO. As this is a community resource, they encourage everyone to upload their own images, contribute comments to images and send them their feedback. Please feel free to use any of the SOAP/WSDL web services. (under development)
Proper citation: Pathbase (RRID:SCR_006141) Copy
http://interactome.baderlab.org/
Project portal for the Human Reference Protein Interactome Project, which aims generate a first reference map of the human protein-protein interactome network by identifying binary protein-protein interactions (PPIs). It achieves this by systematically interrogating all pairwise combinations of predicted human protein-coding genes using proteome-scale technologies.
Proper citation: Human Reference Protein Interactome Project (RRID:SCR_015670) Copy
Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values.
Proper citation: piNET (RRID:SCR_018693) Copy
Web service for querying or retrieving gene annotation data.
Proper citation: MyGene.info (RRID:SCR_018660) Copy
https://cistrome.shinyapps.io/timer/
Web server for comprehensive analysis of tumor infiltrating immune cells. Web tool for systematical analysis of immune infiltrates across diverse cancer types. Allows users to input function specific parameters, with resulting figures dynamically displayed to access tumor immunological, clinical, and genomic features.
Proper citation: TIMER (RRID:SCR_018737) Copy
https://rosie.graylab.jhu.edu/docking2
Unified web framework for Rosetta applications. Web interface for selected Rosetta protocols. Web front end for Rosetta software suite. Provides common user interface for Rosetta protocols, stable application programming interface for developers to add additional protocols, flexible back-end to allow leveraging of computer cluster resources shared by Rosetta Commons member institutions, and centralized administration by Rosetta Commons to ensure continuous maintenance. Offers general and speedy paradigm for serverification of Rosetta applications. Lowers barriers to Rosetta use for broader biological community.
Proper citation: ROSIE (RRID:SCR_018764) Copy
https://delaney.shinyapps.io/CAIRN/
Web tool to graph all copy number alterations present in segment file. Custom data is permitted. Allows to display copy number alterations which overlap user specified region, to quantify number of amplified CNAs and deleted CNAs. Visualization tool to explore copy number alterations discovered in published cancer datasets. Intended to help oncology community observe of relative rates of amplification, deletion, and mutation of interesting genes and regions.
Proper citation: CAIRN (RRID:SCR_019101) Copy
https://immunedb.readthedocs.io/en/latest/
Software system for storing and analyzing high throughput B and T cell immune receptor sequencing data. Comprised of web interface and of Python analysis tools to process raw reads for gene usage, infer clones, aggregate data, and run downstream analyses, or in conjunction with other AIRR tools using its import and export features.
Proper citation: ImmuneDB (RRID:SCR_017125) Copy
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301786/
Device to control spatial and temporal variations in oxygen tensions to better replicate in vivo biology. Consists of three parallel connected tissue chambers and oxygen scavenger channel placed adjacent to these tissue chambers. Provides consistent control of spatial and temporal oxygen gradients in tissue microenvironment and can be used to investigate important oxygen dependent biological processes present in cancer, ischemic heart disease, and wound healing.
Proper citation: Microfluidic device to attain high spatial and temporal control of oxygen (RRID:SCR_017131) Copy
Software tool as data and metadata repository of Extracellular RNA Communication Consortium. Atlas includes small RNA sequencing and qPCR derived exRNA profiles from human and mouse biofluids. All RNAseq datasets are processed using version 4 of exceRpt small RNAseq pipeline. Atlas accepts submissions for RNAseq or qPCR data.
Proper citation: exRNA Atlas (RRID:SCR_017221) Copy
https://www.robotreviewer.net/about
Open source web based system that uses machine learning and NLP to semi automate biomedical evidence synthesis, to aid practice of Evidence Based Medicine. Processes full text journal articles describing randomized controlled trials. Designed to automatically extract key data items from reports of clinical trials.
Proper citation: RobotReviewer (RRID:SCR_021064) Copy
https://github.com/r3fang/SnapATAC
Software package for analyzing scATAC-seq datasets.Used to dissects cellular heterogeneity in unbiased manner and map trajectories of cellular states. Can process data from up to million cells. Incorporates existing tools into comprehensive package for analyzing single cell ATAC-seq dataset.
Proper citation: SnapATAC (RRID:SCR_020981) Copy
https://www.synapse.org/#!Synapse:syn22345748/wiki/605339
Reference dataset of multiplexed immunofluorescence microscopy images collected at HMS Laboratory of Systems Pharmacology. Includes set of images of different types for development and benchmarking of computational methods for image processing. As of 4/2/2021, EMIT comprises tissue microarray containing cores from 34 cancer, non-neoplastic diseases, and normal tissue collected from clinical discards under IRB supervised protocol. TMA was imaged using cyclic immunofluorescence method. Additional extensions of EMIT are currently in the planning stages. Long term goal is to compose ImageNet like resource for highly multiplexed images of tissues and tumors by consolidating high quality curated datasets.
Proper citation: Exemplar Microscopy Images of Tissues (RRID:SCR_021052) Copy
https://appyters.maayanlab.cloud
Collection of web-based software applications that enable users to execute bioinformatics workflows without coding. Turns Jupyter notebooks into fully functional standalone web-based bioinformatics applications. Each Appyter application introduces data entry form for uploading or fetching data, as well as for selecting options for various settings. Once user presses Submit, Appyter is executed in cloud and user is presented with Jupyter Notebook report that contain results. Report includes markdown text, interactive and static figures, and source code. Appyter users can share the link to the output report, as well as download the fully executable notebook for execution on other platforms.
Proper citation: Appyters (RRID:SCR_021245) Copy
https://github.com/abyzovlab/CNVpytor
Software Python package and command line tool for CNV/CNA analysis from depth of coverage by mapped reads. Software tool for CNV/CNA detection and analysis from read depth and allele imbalance in whole genome sequencing.
Proper citation: CNVpytor (RRID:SCR_021627) Copy
https://cumulus.readthedocs.io/en/stable
Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data.
Proper citation: Cumulus (RRID:SCR_021644) Copy
https://github.com/kukionfr/VAMPIRE_open
Software tool for analysis of cell and nuclear morphology from fluorescence or bright field images. Enables profiling and classification of cells into shape modes based on equidistant points along cell and nuclear contours. Robust method to quantify cell morphological heterogeneity.
Proper citation: VAMPIRE (RRID:SCR_021721) Copy
https://github.com/vlink/marge
Software package that integrates genome wide genetic variation with epigenetic data to identify collaborative transcription factor pairs. Optimized to work with chromatin accessibility assays such as ATAC-seq or DNase I hypersensitivity, as well as transcription factor binding data collected by ChIP-seq. Used to identify combinations of cell type specific transcription factors while simultaneously interpreting functional effects of non-coding genetic variation.
Proper citation: Motif Mutation Analysis for Regulatory Genomic Elements (RRID:SCR_021902) Copy
https://github.com/mikelove/tximport
Software R package for importing pseudoaligned reads into R for use with downstream differential expression analysis. Used for import and summarize transcript level estimates for transcript and gene level analysis.
Proper citation: tximport (RRID:SCR_016752) Copy
https://software.broadinstitute.org/cancer/cga/polysolver
Software tool for HLA typing based on whole exome sequencing data and infers alleles for three major MHC class I genes. Enables accurate inference of germline alleles of class I HLA-A, B and C genes and subsequent detection of mutations in these genes using inferred alleles as reference.
Proper citation: Polysolver (RRID:SCR_022278) Copy
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