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https://github.com/wenmm/EssSubgraph/tree/main
A model algorithm that integrates omics data and network data to predict essential genes.
Proper citation: EssSubgraph (RRID:SCR_027354) Copy
An American pharmaceutical company aiming to make a difference in the lives of people globally through their medicines, vaccines, biologic therapies and animal health products.
Proper citation: Merck (RRID:SCR_001287) Copy
http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/somaticcall-manual
Software program that finds single-base differences (substitutions) between sequence data from tumor and matched normal samples. It is designed to be highly stringent, so as to achieve a low false positive rate. It takes as input a BAM file for each sample, and produces as output a list of differences (somatic mutations). Note: This software package is no longer supported and information on this page is provided for archival purposes only.
Proper citation: SomaticCall (RRID:SCR_001196) Copy
http://patchwork.r-forge.r-project.org/
Software tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which enables characterization of genomic alterations ranging in size from point mutations to entire chromosomes. High quality results are obtained even if samples have low coverage, ~4x, low tumor cell content or are aneuploid. Patchwork takes BAM files as input whereas PatchworkCG takes input from CompleteGenomics files. TAPS performs the same analysis as Patchwork but for microarray data.
Proper citation: Patchwork (RRID:SCR_000072) Copy
http://www.mmnt.net/db/0/0/ftp-genome.wi.mit.edu/distribution/GISTIC2.0
Software to identify genes targeted by somatic copy-number alterations (SCNAs) that drive cancer growth. By separating SCNA profiles into underlying arm-level and focal alterations, they improve the estimation of background rates for each category.
Proper citation: GISTIC (RRID:SCR_000151) Copy
A contract research organization (CRO) specializing in preclinical oncology services. As a pioneer in the field of patient derived tumor xenografts (PDX), they provide tailored solutions to the problems faced by preclinical oncology researchers. They assist with the identification of the best drug candidates and the validation of their targets and deliver in-depth bioinformatics analyses, laying the groundwork for the successful planning of clinical trials. Their diverse tumor model collection enables them to recommend the right assays and models to answer their customers' questions. Their AAALAC accredited facilities with IVC system, separate model development unit, large cage capacity of over 14,500 mice and proprietary electronic measurement system with an integrated database and by continuously maintaining important PDX models in mice, they are able to provide the highest standard of testing within a reasonable timeframe.
Proper citation: Oncotest (RRID:SCR_000489) Copy
http://www.broadinstitute.org/cancer/cga/mutect
Software for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.
Proper citation: MuTect (RRID:SCR_000559) Copy
A cancer research center whose goal is to offer innovative technoligies to spur the develpment of new methods of diagnosing and treating cancer. CNIO contains a variety of programs of investigation, including a biotechnology program, a clinical research program, and a molecular oncology program. CNIO also provides services that allow researchers to access and use technologies and tools such as cytogenetics and monoclonal antibodies, and hosts a biomedical biobank.
Proper citation: Spanish National Cancer Research Center (RRID:SCR_014054) Copy
Ratings or validation data are available for this resource
http://pubs.rsc.org/en/content/articlehtml/2017/LC/C7LC00703E
Equipment that is a magnetic micropore chip for rapid unbiased circulating tumor cell isolation and in situ RNA analysis. The chip detects tumor cells and can help doctors treat patients with these tumors.
Proper citation: CaTCh FISH Chip (RRID:SCR_015810) Copy
http://bioinfo-out.curie.fr/projects/snp_gap/
Software for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured by single-nucleotide polymorphism (SNP) arrays. The method is based on pattern recognition of segmented and smoothed copy number and allelic imbalance profiles. The method performs well even for poor-quality data, low tumor content, and highly rearranged tumor genomes.
Proper citation: Genome Alteration Print (RRID:SCR_012016) Copy
Biomedical research institute in Germany that investigates the mechanisms of cancer and works to identify cancer risk factors. They provide the foundations for developing novel approaches in the prevention, diagnosis, and treatment of cancer and are a member of the Helmholtz Association of National Research Centers. Professor Harald zur Hausen was awarded the Nobel Prize for Medicine for his outstanding scientific contribution to the study of human papillomaviruses (HPV). In addition, the staff of the Cancer Information Service (KID) offers information about the widespread disease of cancer for patients, their families, and the general public. The Center is funded by the German Federal Ministry of Education and Research (90%) and the State of Baden-Württemberg (10%).
Proper citation: German Cancer Research Center (RRID:SCR_012942) Copy
Fund the best research to eradicate diseases and support the warfighter to benefit the American Public. They promote innovative research, recognizing untapped opportunities, creating partnerships, and guarding the public trust. Research Program topics include: * Amyotrophic Lateral Sclerosis * Autism * Bone Marrow Failure * Breast Cancer * Defense Medical Research and Development Program * Duchenne Muscular Dystrophy * Gulf War Illness * Lung Cancer * Multiple Sclerosis * Neurofibromatosis * Ovarian Cancer * Peer Reviewed Cancer * Peer Reviewed Medical * Peer Reviewed Orthopaedic * Prostate Cancer * Psychological Health / Traumatic Brain Injury * Spinal Cord Injury * Tuberous Sclerosis Complex
Proper citation: Congressionally Directed Medical Research Program (RRID:SCR_006456) Copy
Open access resource for human proteins. Used to search for specific genes or proteins or explore different resources, each focusing on particular aspect of the genome-wide analysis of the human proteins: Tissue, Brain, Single Cell, Subcellular, Cancer, Blood, Cell line, Structure and Interaction. Swedish-based program to map all human proteins in cells, tissues, and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics, and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome.
Proper citation: The Human Protein Atlas (RRID:SCR_006710) Copy
The Terry Fox Foundation is responsible for supporting close to $20 million in discovery based research each year in Canada - all monies raised outside Canada must be distributed to (a) an institute approved by the Foundation and its advisors or (b) remitted to Canada. The Terry Fox Research Institute (TFRI) is a recipient of TFF funding for translational research. TFRI is an exciting new initiative whose goal is to translate rapidly today''s best science into better cancer treatment and diagnosis for all Canadians. The Institute will bring scientists and clinicians together across the country into a functionally integrated, geographically dispersed Institute with nodes in several provinces. Terry Fox was diagnosed with osteogenic sarcoma (bone cancer) in his right leg in 1977 and had his leg amputated 15 cm (six inches) above the knee. While in hospital, Terry was so overcome by the suffering of other cancer patients that he decided to run across Canada to raise money for cancer research. He called his journey the Marathon of Hope. Terry''s Marathon of Hope took place in 1980 with the simple objective of informing Canadians of the importance of finding a cure for cancer. With fierce determination, he ran an average of 42 kilometres (26 miles) every day for 143 days. Terry was forced to end his run on September 1, 1980 when the cancer spread to his lungs. By February 1, 1981, Terry''s dream of raising $1 for every Canadian was realized - the Terry Fox Marathon of Hope fund totaled $24.17 million. Terry died in June 1981. On May 26, 1988, The Terry Fox Run became a Trust, independent from the Canadian Cancer Society, and received tax-exempt charitable registration as a public foundation. In addition to our signature and long-standing National Terry Fox Run Day in September of each year, The Terry Fox Foundation is proud to include in its events portfolio The National School Run Day. The Foundation recognizes the duality of its mandate. Not only does it raise money for research, but it also continues to share the story of Terry Fox. The Terry Fox Foundation strives to maintain the heroic effort and integrity that Terry embodied. It is a grassroots organization that does not allow the Terry Fox name or likeness to be commercialized or conjoined with other worthy causes. To date, over $600 million has been raised worldwide for cancer research in Terry''s name.
Proper citation: Terry Fox Foundation (RRID:SCR_005873) Copy
The Advanced Centre for Treatment, Research and Education in Cancer (ACTREC) is the new state-of-the-art R&D satellite of the Tata Memorial Centre (TMC), which also includes under its umbrella the Tata Memorial Hospital (TMH), the largest cancer hospital in Asia. ACTREC has the mandate to function as a national centre for treatment, research and education in cancer. TMC is an autonomous grant-in-aid institution of the Department of Atomic Energy (DAE), Government of India. It is registered under the Societies Registration Act (1860) and the Bombay Public Trust Act (1950). Its Governing Council is headed by the Chairman, Atomic Energy Commission, Government of India. ACTREC comprises of 2 arms - one for basic research and another for clinical research. The basic research building was inaugurated in March 2002 at the new site of ACTREC in Kharghar, Navi Mumbai. In August 2002, the Cancer Research Institute (CRI) shifted in toto from its Parel campus in Mumbai to serve as the basic research arm of ACTREC. The clinical research arm of ACTREC comprising of the Clinical Research Centre (CRC) has become functional from March 2005. ACTREC also has a 50-bed hospital fully equipped with state-of-the-art diagnostic and therapeutic facilities. Research investigations at CRI currently focus on molecular mechanisms responsible for causation of major human cancers relevant to India. It is envisaged that in the future, ACTREC will play a greater role in drug development and emerging therapies for treatment and prevention of cancer.
Proper citation: ACTREC - Advanced Centre for Treatment Research and Education in Cancer (RRID:SCR_006021) Copy
http://thelongevityfoundation.org/
Funding resource that supports research into A-T (Ataxia Telangiectasia) and other debilitating, degenerative diseases plaguing human kind, including cancer and neuro-degeneration associated with auto-immunity and aging. Researchers share their findings and collaborate with each other. The research must lead to practical, near-term treatments and cures to receive funds. The researchers have found treatments and cures that are the first of their kind in the world. Over $850,000 in direct research grants have been made. These grants have leveraged over $9 million in research resources contributed by partner institutions. We pay the research institutions for direct costs only. We pay no administrative, indirect, or overhead costs.
Proper citation: Longevity Foundation (RRID:SCR_006338) Copy
http://www.uni-koeln.de/med-fak/cgars/
Software package to dissect random from non-random patterns in copy number data and thereby to assess significantly enriched somatic copy number aberrations (SCNA) across a set of tumor specimens or cell lines.
Proper citation: CGARS (RRID:SCR_006404) Copy
http://bioinf.wehi.edu.au/socrates/
Software for detecting genomic rearrangements in tumors that utilizes only split-read data. It features single nucleotide resolution, high sensitivity, and high specificity in simulated data. It takes advantage of parallelism for efficient use of resources.
Proper citation: Socrates (RRID:SCR_006411) Copy
Statistical software to estimate tumor purity, ploidy and absolute copy numbers from next generation sequencing data.
Proper citation: AbsCN-seq (RRID:SCR_006409) Copy
http://www.c2b2.columbia.edu/danapeerlab/html/jistic.html
Software tool for analyzing datasets of genome-wide copy number variation to identify driver aberrations in cancer.
Proper citation: JISTIC (RRID:SCR_003482) Copy
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