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https://geopandas.org/en/stable/
Software open-source Python library that makes it easy to work with geospatial data. It extends the popular data analysis library, Pandas, by allowing you to perform spatial operations on geometric shapes like points, lines, and polygons.
Proper citation: GeoPandas (RRID:SCR_028590) Copy
Software package installer for Python. You can use pip to install packages from the Python Package Index and other indexes.
Proper citation: pip (RRID:SCR_028591) Copy
https://github.com/openvax/mhcflurry
Software MHC I ligand prediction package with competitive accuracy and documented implementation. Used for peptide-MHC I binding affinity prediction.
Proper citation: mhcflurry (RRID:SCR_028577) Copy
https://github.com/VanLoo-lab/ASCAT.sc
Software application as implementation of ASCAT allowing generation of CNV profiles from single cell and short coverage sequencing data.
Proper citation: ASCAT sc (RRID:SCR_028613) Copy
https://github.com/markowetzlab/CINSignatureQuantification
Software R package to quantify the activity of signatures of chromosomal instability from absolute copy number profiles. Used to quantifying copy number signatures from absolute copy number profiles.
Proper citation: CINSignatureQuantification (RRID:SCR_028614) Copy
Spacial neuron gene expression atlas. Interactive, server-free web application and spatial transcriptomics database designed to help researchers map and analyze gene expression within the brain. Mouse whole brain spatial transcriptomic atlas.
Proper citation: PANGEA (RRID:SCR_028559) Copy
http://babylone.ulb.ac.be/BeAtMuSiC/
Web tool for prediction of changes in protein-protein binding affinity on mutations. Predictor of changes in binding free energy induced by point mutations. It relies on a set of statistical potentials derived from known protein structures, and combines the effect of the mutation on the strength of the interactions at the interface, and on the overall stability of the complex.
Proper citation: BeAtMuSiC (RRID:SCR_028562) Copy
https://bioconductor.org/packages/genomation/
Software R package for simplfiying common tasks in genomic feature analysis. Toolkit to summarize, annotate and visualize genomic intervals. Provides functions for reading BED and GFF files as GRanges objects, summarizing genomic features over predefined windows so users can make average enrichment of features over defined regions or produce heatmaps. Can annotate given regions with other genomic features such as exons,introns and promoters.
Proper citation: genomation (RRID:SCR_003435) Copy
An international coalition formed to enable the sharing of genomic and clinical data to help unlock potential advancements in medicine and science. Bringing together more than 145 leading institutions working in healthcare, research, disease advocacy, life science, and information technology, the Global Alliance is working together to create and promulgate harmonized approaches to enable the responsible, voluntary, and secure sharing of genomic and clinical data.
Proper citation: Global Alliance for Genomics and Health (RRID:SCR_003555) Copy
http://www.genabel.org/packages/MetABEL
Software for meta-analysis of genome-wide SNP association results.
Proper citation: MetABEL (RRID:SCR_003429) Copy
http://www.eurodiagnostica.com/
Antibody supplier.
Proper citation: Euro-Diagnostica (RRID:SCR_003421) Copy
The RNA modification database provides a comprehensive listing of posttranscriptionally modified nucleosides from RNA. Information provided for each nucleoside includes: the type of RNA in which it occurs and phylogenetic distribution; common chemical name and symbol; Chemical Abstracts registry number and index name; chemical structure; initial literature citations for structural characterization or occurrence, and for chemical synthesis. Both the structural diversity and extent of posttranscriptional modification in RNA is remarkable, with 107 different nucleosides presently known in all types of RNA. The discovery of new modified nucleosides as well as increasing knowledge of the array of functional roles of modification, based largely on extensive studies of tRNA, mandates a need for a comprehensive database of RNA nucleosides. The RNA Modification Database is maintained as an extension of the initial version published in mid-1994. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA. The information provided permits access to the modified nucleoside literature through provision of both computer-searchable Chemical Abstracts registry numbers and key literature citations. This database also provides an historical record of the initial reports of occurrence, characterization and chemical synthesis of modified nucleosides from RNA. It is our judgement that the total number of RNA nucleosides listed, and the chemical structures reported, are very accurate. However, the distributions listed are in some cases a matter of concern, due primarily to the possibility of inhomogeneity of the RNA isolate and the use of methods of nucleoside identification that are not sufficiently rigorous. Reinvestigation of some of the unusual or single-report source distributions is warranted, and will likely lead to future refinements in the listings. The authors invite comments concerning new entries, errors or omissions and on the format presently used for electronic access to the database.
Proper citation: RNA Modification Database (RRID:SCR_003535) Copy
https://github.com/dbitton/LaSSO
An R script that creates a FASTA database containing all possible lariat signatures from a given set of introns.
Proper citation: LaSSO (RRID:SCR_003418) Copy
http://www.metafor-project.org/doku.php
A free and open-source add-on for conducting meta-analyses with the statistical software environment R.
Proper citation: metaphor (RRID:SCR_003450) Copy
Database of protein families and domains that is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, on the basis of similarities in their sequences, into a limited number of families. Proteins or protein domains belonging to a particular family generally share functional attributes and are derived from a common ancestor. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. ScanProsite finds matches of your protein sequences to PROSITE signatures. PROSITE currently contains patterns and profiles specific for more than a thousand protein families or domains. Each of these signatures comes with documentation providing background information on the structure and function of these proteins. The database is available via FTP.
Proper citation: PROSITE (RRID:SCR_003457) Copy
An Antibody supplier
Proper citation: Everest Biotech (RRID:SCR_003456) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/minfi.html
Software that improves the results from the Illumina infinium HumanMethylation450 BeadChips by reducing technical variation within and between arrays. SWAN is available in the minfi Bioconductor package.
Proper citation: SWAN (RRID:SCR_003455) Copy
https://code.google.com/p/bmiq/
Software using a beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data.
Proper citation: BMIQ (RRID:SCR_003446) Copy
A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context.
Proper citation: GEPAT (RRID:SCR_003597) Copy
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