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Software application as an open source Pyton library to search and predict miRNA targets.
Proper citation: miRmap (RRID:SCR_016508) Copy
http://bioinf.bio.uth.gr/nat-ncs2
Web server for the detection and evolutionary classification of prokaryotic and eukaryotic nucleobase-cation symporters of the NAT/NCS2 family. Used to scan, identify and evolutionary classify NAT/NCS2 nucleobase transporter proteins.
Proper citation: NAT/NCS2 Hound (RRID:SCR_016473) Copy
http://jefferis.github.io/nat/
Software R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons in the context of 3D brain structures.
Proper citation: NeuroAnatomy Toolbox (RRID:SCR_016716) Copy
http://projects.biotec.tu-dresden.de/metapocket/
Software tool to identify pockets on protein surface to predict ligand-binding sites.
Proper citation: metaPocket (RRID:SCR_016653) Copy
Software assembler and analysis tool for whole-genome short-gun sequencing for Illumina reads. Provides tools for error correction, sequence-to-read alignment and comparison between read sets. Used for large genomes.
Proper citation: fermi (RRID:SCR_016652) Copy
https://github.com/WilsonSayresLab/XYalign
Software tool for identifying, understanding, and correcting technical biases on the sex chromosomes in next generation sequencing data.
Proper citation: XYalign (RRID:SCR_016661) Copy
http://www.ccb.jhu.edu/software/centrifuge/
Software for rapid and sensitive classification of metagenomic sequences. Used for the classification of DNA sequences from microbial samples and analysis of large metagenomics data sets on conventional desktop computers.
Proper citation: Centrifuge Classifier (RRID:SCR_016665) Copy
Software as graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics.
Proper citation: NMRProcFlow (RRID:SCR_016592) Copy
https://www.ncbi.nlm.nih.gov/projects/mutagene/
Software tool to explore and analyze mutagenic factors leading to tumors to decipher cancer genetic heterogeneity.
Proper citation: MutaGene (RRID:SCR_016574) Copy
https://blake.bcm.edu/emanwiki/EMAN2
Software suite for processing data from transmission electron microscopes. Used in supercomputing facilities as a test application for large-scale computing. Used for single particle reconstruction, helical reconstruction, 2-D crystallography and whole-cell tomography.
Proper citation: EMAN (RRID:SCR_016867) Copy
Software R package for calculating, applying, evaluating and plotting results of polygenic risk scores analysis. Performs simulation study to estimate P value significance threshold for high resolution PRS studies and produces plots for inspection of results. Operating Unix/Linux.
Proper citation: PRSice (RRID:SCR_017057) Copy
Software tool to create and provide heat maps through a graphical interface. Allows to create an expression, pairwise comparison, image overlay, geomap, and geocoordinate heat maps for different data types and applications. Used to interactively visualize data.
Proper citation: Heatmapper (RRID:SCR_016974) Copy
https://github.com/macmanes-lab/BinPacker/blob/master/README
Software tool as de novo trascriptome assembler for RNA-Seq data. Used to assemble full length transcripts by remodeling problem as tracking set of trajectories of items over splicing graph. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux.
Proper citation: BinPacker (RRID:SCR_017038) Copy
https://github.com/INTABiotechMJ/MITE-Tracker
Open source software tool for identifying miniature inverted repeat transposable elements in large genomes. Used to process large scale genomes, to find and classify MITEs using an efficient alignment strategy to retrieve nearby inverted repeat sequences.
Proper citation: MITE-Tracker (RRID:SCR_017030) Copy
https://github.com/Rinoahu/SwiftOrtho
Software tool for orthology analysis to identify orthologs, paralogs and co orthologs for genomes. Used to perform homology classification across genomes of different species in large genomic datasets.
Proper citation: SwiftOrtho (RRID:SCR_017122) Copy
Issue
https://biit.cs.ut.ee/clustvis/
Web user interface for visualizing clustering of multivariate data. Web server allows users to upload their own data and create Principal Component Analysis plots and heatmaps.
Proper citation: ClustVis (RRID:SCR_017133) Copy
http://rtools.cbrc.jp/centroidfold/
Web server for RNA secondary structure prediction. Predicts RNA secondary structure from RNA sequence. Based on generalized centroid estimator.
Proper citation: CentroidFold (RRID:SCR_017253) Copy
https://github.com/ruanjue/wtdbg2.git
Software tool as de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies. It assembles raw reads without error correction and then builds consensus from intermediate assembly output. Desiged to assemble huge genomes in very limited time.
Proper citation: WTDBG (RRID:SCR_017225) 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_017228) Copy
https://github.com/csbbcompbio/CSBB-v3.0
Software package for analysis of sequencing data. Command line based bioinformatics suite to analyze biological data acquired through biological experiments.
Proper citation: Computational Suite for Bioinformaticians and Biologists (RRID:SCR_017234) Copy
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