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https://github.com/FRED-2/OptiType
Software tool for precision HLA typing from next generation sequencing data.
Proper citation: OptiType (RRID:SCR_022279) Copy
http://rrwick.github.io/Bandage/
Software tool for visualising de novo assembly graphs. By displaying connections which are not present in contigs file, opens up new possibilities for analysing de novo assemblies. Used for interactive visualization of de novo genome assemblies.
Proper citation: Bandage (RRID:SCR_022772) Copy
A web application to assist in the identification of articles and research related to literature search terms. The search covers full text articles in the Europe PMC repository. Relevant papers are suggested to users based on the scientific term searched and the selection of questions, generated by the application, relevant to term searched.
Proper citation: EvidenceFinder (RRID:SCR_013764) Copy
Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron.
Proper citation: MRIcron (RRID:SCR_002403) Copy
https://www.sanger.ac.uk/science/tools/caf
Software tools for manipulating Common Assembly Format files text format for describing sequence assemblies,that can be downloaded from the Sanger ftp site.
Proper citation: caftools (RRID:SCR_023982) Copy
https://data.broadinstitute.org/alkesgroup/BOLT-LMM/
Software statistical tool for identifying genetic associations. Used for genome wide association studies in large cohorts.
Proper citation: BOLT-LMM (RRID:SCR_023978) Copy
http://contra.stanford.edu/contrafold/
Software novel secondary structure prediction method based on conditional log-linear models, a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. Used for sequence prediction.
Proper citation: CONTRAfold (RRID:SCR_023994) Copy
http://ingenium.home.xs4all.nl/dicom.html
Software for DICOM training and testing,Demonstration and research image archives,Image format conversion from scanner with DICOM network access,DICOM image viewing and slide making, DICOM image selection, (limited) editing, and splitting and merging of series, Advanced scriptable image modification, filtering, forwarding and conversion, DICOM caching and archive merging, DICOM web access for viewing and data management (scriptable),Connection to Lua IDE for all sorts of DICOM manipulation.
Proper citation: Conquest DICOM (RRID:SCR_023993) Copy
Software tool designed to simplify Multivariate analysis (correspondence analysis) of codon and amino acid usage. It also calculates standard indices of codon usage.
Proper citation: CodonW (RRID:SCR_023989) Copy
https://github.com/pennsignals/chime
Software designed to assist hospitals and public health officials with understanding hospital capacity needs as they relate to the COVID pandemic. CHIME enables capacity planning by providing estimates of total daily and running totals of inpatient hospitalizations, ICU admissions, and patients requiring ventilation.
Proper citation: CHIME (RRID:SCR_023987) Copy
https://genome.sph.umich.edu/wiki/EMMAX
Software statistical test for large scale human or model organism association mapping accounting for the sample structure. In addition to the computational efficiency obtained by EMMA algorithm, EMMAX takes advantage of the fact that each loci explains only a small fraction of complex traits, which allows us to avoid repetitive variance component estimation procedure, resulting in a significant amount of increase in computational time of association mapping using mixed model.
Proper citation: EMMAX (RRID:SCR_024012) Copy
https://biocore.github.io/emperor/
Web browser enabled tool with versatile command line interface to perform exploratory investigations of 3D visualizations of microbial community data, such as principal coordinates plots. EMPeror includes set of controllers to modify features as function of metadata. Web interactive next generation tool for analysis, visualization and understanding of high throughput microbial ecology datasets.
Proper citation: EMPeror (RRID:SCR_024013) Copy
https://embossgui.sourceforge.net/
Web based graphical user interface to the EMBOSS suite of bioinformatics tools.
Proper citation: EMBOSS explorer (RRID:SCR_024014) Copy
Software extensible open source radiation therapy research platform based on the DICOM standard. It also functions as a cross-platform DICOM RT viewer.
Proper citation: dicompyler (RRID:SCR_024006) Copy
https://github.com/rrwick/Filtlong
Software tool for filtering long reads by quality.Can take set of long reads and produce smaller, better subset. Uses both read length and read identity when choosing which reads pass the filter.
Proper citation: Filtlong (RRID:SCR_024020) Copy
https://cran.r-project.org/web/packages/foreign/index.html
Software tool for reading and writing data stored by some versions of 'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', and for reading and writing some 'dBase' files.
Proper citation: foreign (RRID:SCR_024025) Copy
https://github.com/rrwick/Deepbinner
Software tool for demultiplexing barcoded Oxford Nanopore sequencing reads.Signal level demultiplexer for Oxford Nanopore reads.
Proper citation: Deepbinner (RRID:SCR_024001) Copy
Software tool to simulate process of transmitting X-rays through phantom objects. Reconstructs original phantom image from projections. Has wide array of image analysis and image processing functions.
Proper citation: CTSim (RRID:SCR_024004) Copy
https://github.com/qmarcou/IGoR/
C++ software designed to infer V(D)J recombination related processes from sequencing data.
Proper citation: IGoR (RRID:SCR_024053) Copy
http://wasabiapp.org/software/prank/
Software application as probabilistic multiple alignment program for DNA, codon and amino-acid sequences. Allows for defining potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences.
Proper citation: PRANK (RRID:SCR_024174) Copy
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