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https://github.com/pinellolab/CRISPResso2

Software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments. Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments.

Proper citation: CRISPResso2 (RRID:SCR_024503) Copy   

•   Source: SciCrunch Registry
  

https://silebat.github.io/FSK-Lab/openbugs.html

Software for analysing complex statistical models using Markov chain Monte Carlo methods.

Proper citation: OpenBUGS (RRID:SCR_024488) Copy   

•   Source: SciCrunch Registry
  

https://github.com/bzhanglab/AutoRT/

Software tool for peptide retention time prediction using deep learning. Supports peptide retention prediction for tryptic peptides, MHC bound peptides and PTM peptides.

Proper citation: AutoRT (RRID:SCR_024513) Copy   

•   Source: SciCrunch Registry
  

https://www.reading.ac.uk/bioinf/ModFOLD/

Web server for the global and local quality estimation of 3D protein models

Proper citation: ModFOLD (RRID:SCR_024518) Copy   

•   Source: SciCrunch Registry
  

http://metscape.ncibi.org

A software program that allows users to visualize and interpret human metabolim and expression profiling data by providing users with a bioinformatics framework. Its features include bulding and analyzing networks of genes and compounds, identifying enriched pathways from expression profiling data, and visualizing changes in metabolite data.

Proper citation: Metscape (RRID:SCR_014687) Copy   

•   Source: SciCrunch Registry
  

http://www.bic.mni.mcgill.ca/software/minc/

A medical imaging data format and an associated set of tools and libraries including a 3 level API for medical image analysis with a particular focus on the needs of research. There are also a number of tools including Registration and Non-Uniformity correction.

Proper citation: MINC (RRID:SCR_002391) Copy   

•   Source: SciCrunch Registry
  

https://www.cdc.gov/epiinfo/

Software suite of interoperable software tools designed for global community of public health practitioners and researchers. Provides easy data entry form and database construction, customized data entry experience, and data analysis with epidemiologic statistics, maps, and graphs for public health professionals who may lack information technology background.Statistical software for epidemiology developed by Centers for Disease Control and Prevention in Atlanta, Georgia. Available for Microsoft Windows, Android and iOS, along with web and cloud version.

Proper citation: Epi Info (RRID:SCR_021682) Copy   

•   Source: SciCrunch Registry
  

https://business-lounge.heidelbergengineering.com/de/de/products/heidelberg-eye-explorer/

Platform that centralizes management of ophthalmic images. HEYEX interfaces with electronic medical record systems and third-party devices to allow exchange, storage, and dynamic review of diagnostic images. Heidelberg Engineering imaging products use Heidelberg Eye Explorer software platform and database to store patient information and images.

Proper citation: Heidelberg Eye Explorer (RRID:SCR_022045) Copy   

•   Source: SciCrunch Registry
  

http://www.mathworks.com/products/matlab/

Multi paradigm numerical computing environment and fourth generation programming language developed by MathWorks. Allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, Java, Fortran and Python. Used to explore and visualize ideas and collaborate across disciplines including signal and image processing, communications, control systems, and computational finance.

Proper citation: MATLAB (RRID:SCR_001622) Copy   

•   Source: SciCrunch Registry
  

https://imagej.net/

Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets.

Proper citation: ImageJ (RRID:SCR_003070) Copy   

•   Source: SciCrunch Registry
  

http://penglab.janelia.org/proj/v3d/V3D/About_V3D.html

V3D is a handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. It also provides many unique functions, is Open Source, supports a very simple and powerful plugin interface and thus can be extended & enhanced easily. V3D-Neuron is a powerful 3D neuron reconstruction, visualization, and editing software built on top of V3D. Both V3D and V3D-Neuron have recently been published in Nature Biotechnology (April, 2010), and Highlighted in Nature Methods (May, 2010), and Science News (April, 2010), etc. V3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. This makes V3D suitable for various bioimage informatics applications, and a nice platform to develop new 3D image analysis algorithms for high-throughput processing. In short, V3D streamlines the workflow of visualization-assisted analysis. In the latest V3D development, it can render 5D (spatial-temporal) data directly in 3D volume-rendering mode; it supports convenient and interactive local and global 3D views at different scales. It even has a Matlab file IO toolbox. A user can now write his/her own plugins to take advantage of the V3D platform very easily.

Proper citation: V3D (RRID:SCR_008646) Copy   

•   Source: SciCrunch Registry
  

http://www.ebi.ac.uk/Tools/sss/fasta/

Software package for DNA and protein sequence alignment to find regions of local or global similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence.

Proper citation: FASTA (RRID:SCR_011819) Copy   

•   Source: SciCrunch Registry
  

http://scholar.google.com/

Google Scholar provides a simple way to broadly search for scholarly literature. From one place, you can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites. Google Scholar helps you find relevant work across the world of scholarly research. Features of Google Scholar * Search diverse sources from one convenient place * Find articles, theses, books, abstracts or court opinions * Locate the complete document through your library or on the web * Learn about key scholarly literature in any area of research How are documents ranked? Google Scholar aims to rank documents the way researchers do, weighing the full text of each document, where it was published, who it was written by, as well as how often and how recently it has been cited in other scholarly literature. * Publishers - Include your publications in Google Scholar * Librarians - Help patrons discover your library''s resources

Proper citation: Google Scholar (RRID:SCR_008878) Copy   

•   Source: SciCrunch Registry
  

http://tcoffee.crg.cat/apps/tcoffee/do:regular

A multiple sequence alignment server which can align Protein, DNA and RNA sequences.

Proper citation: T-Coffee (RRID:SCR_011818) Copy   

•   Source: SciCrunch Registry
  

http://probcons.stanford.edu/

Efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.

Proper citation: ProbCons (RRID:SCR_011813) Copy   

•   Source: SciCrunch Registry
  

http://genevenn.sourceforge.net/

A web application creating Venn diagrams from two or three gene lists.

Proper citation: GeneVenn (RRID:SCR_012117) Copy   

•   Source: SciCrunch Registry
  

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome

Tool to search translated nucleotide databases using a protein query.

Proper citation: TBLASTN (RRID:SCR_011822) Copy   

•   Source: SciCrunch Registry
  

http://nhjy.hzau.edu.cn/kech/swxxx/jakj/dianzi/Bioinf6/GeneFinding/GeneFinding2.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 10,2020. Data analysis service for Hidden Markov Model (HMM)-based gene structure prediction (multiple genes, both chains).

Proper citation: FGENESH (RRID:SCR_011928) Copy   

•   Source: SciCrunch Registry
  

http://gpcr.biocomp.unibo.it/bacello/

A predictor for the subcellular localization of proteins in eukaryotes that is based on a decision tree of several support vector machines (SVMs). It classifies up to four localizations for Fungi and Metazoan proteins and five localizations for Plant ones. BaCelLo's predictions are balanced among different classes and all the localizations are considered as equiprobable.

Proper citation: BaCelLo (RRID:SCR_011965) Copy   

•   Source: SciCrunch Registry
  

http://Mar2008.archive.ensembl.org

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17,2022. Genome databases for vertebrates and other eukaryotic species. Analysis and annotation maintained on current data.Distribution of analysis to other bioinformatics laboratories. Ensembl concentrates on vertebrate genomes, but other groups have adapted system for use with plant and fungal genomes (see Powered by Ensembl list on website).

Proper citation: Ensembl Genome Browser (RRID:SCR_013367) Copy   

•   Source: SciCrunch Registry