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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
Web service for querying or retrieving gene annotation data.
Proper citation: MyGene.info (RRID:SCR_018660) 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
Database of traceable, standardized, annotated gene signatures which have been manually curated from publications that are indexed in PubMed. The Advanced Gene Search will perform a One-tailed Fisher Exact Test (which is equivalent to Hypergeometric Distribution) to test if your gene list is over-represented in any gene signature in GeneSigDB. Gene expression studies typically result in a list of genes (gene signature) which reflect the many biological pathways that are concurrently active. We have created a Gene Signature Data Base (GeneSigDB) of published gene expression signatures or gene sets which we have manually extracted from published literature. GeneSigDB was creating following a thorough search of PubMed using defined set of cancer gene signature search terms. We would be delighted to accept or update your gene signature. Please fill out the form as best you can. We will contact you when we get it and will be happy to work with you to ensure we accurately report your signature. GeneSigDB is capable of providing its functionality through a Java RESTful web service.
Proper citation: GeneSigDB (RRID:SCR_013275) Copy
http://www.rhesusbase.org/drugDisc/CAM.jsp
OKCAM (Ontology-based Knowledgebase for Cell Adhesion Molecules) is an online resource for human genes known or predicted to be related to the processes of cell adhesion. These genes include members of the cadherin, immunoglobulin/FibronectinIII (IgFn), integrin, neurexin, neuroligin, and catenin families. Totally 496 human CAM genes were compiled and annotated. We have mapped these genes onto a novel cell adhesion molecule ontology (CAMO) that provides a hierarchical description of cell adhesion molecules and their functions. It is intended to provide a means to facilitate better and better understanding of the global and specific properties of CAMs through their genomic features, regulatory modes, expression patterns and disease associations become clearer. You may browse by CAM ontology, Chromosomes and Full Gene list.
Proper citation: OKCAM: Ontology-based Knowledgebase for Cell Adhesion Molecules (RRID:SCR_010696) Copy
https://genome-cancer.ucsc.edu/
A suite of web-based tools to visualize, integrate and analyze cancer genomics and its associated clinical data. It is possible to display your own clinical data within one of their datasets.
Proper citation: UCSC Cancer Genomics Browser (RRID:SCR_011796) Copy
A web-based application designed with an easy-to-use interface to facilitate the high-throughput assessment and prioritization of genes and missense alterations important for cancer tumorigenesis.
Proper citation: CRAVAT (RRID:SCR_012776) 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://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/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/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
http://amp.pharm.mssm.edu/LJP/
Interactive on line tool where signatures are tagged with user selected metadata and external transcript signatures are projected onto network. Browser to visualize signatures from breast cancer cell lines treated with single molecule perturbations.
Proper citation: LINCS Joint Project - Breast Cancer Network Browser (RRID:SCR_016181) Copy
https://github.com/jbelyeu/SV-plaudit
Software for rapidly curating structural variant (SVs) predictions. SV-plaudit provides a pipeline for creating image views of genomic intervals, automatically storing them in the cloud, deploying a website to view/score them, and retrieving scores for analysis.
Proper citation: SV-plaudit (RRID:SCR_016285) Copy
http://amp.pharm.mssm.edu/DGB/
Web based application to assist researchers with identifying drugs and small molecules that are predicted to maximally influence expression of mammalian gene of interest. Used to identify drugs and small molecules to regulate expression of target genes for research purpose only. Application for ranking drugs to modulate specific gene based on transcriptomic signatures.
Proper citation: Drug Gene Budger (RRID:SCR_016489) Copy
https://github.com/dpeerlab/phenograph
Software tool as clustering method designed for high dimensional single cell data. Algorithmically defines phenotypes in high dimensional single cell data. Used for large scale analysis of single cell heterogeneity.
Proper citation: Phenograph (RRID:SCR_016919) Copy
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