Tools   Select Another Resource Report Type

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   

•   Source: SciCrunch Registry

https://github.com/lh3/fermi

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://prsice.info/

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   

•   Source: SciCrunch Registry

http://www2.heatmapper.ca/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/alyssafrazee/polyester

An R package designed to simulate RNA sequencing experiments with differential transcript expression. Given a set of annotated transcripts, it will simulate the steps of an RNA-seq experiment (fragmentation, reverse-complementing, and sequencing) and produce files containing simulated RNA-seq reads. Simulated reads can be analyzed using a choice of downstream analysis tools. Polyester has a built-in wrapper function to simulate a case/control experiment with differential transcript expression and biological replicates. Users are able to set the levels of differential expression at transcripts of their choosing. This means they know which transcripts are differentially expressed in the simulated dataset, so accuracy of statistical methods for differential expression detection can be analyzed. Polyester offers several unique features: * Built-in functionality to simulate differential expression at the transcript level * Ability to explicitly set differential expression signal strength * Simulation of small datasets, since large RNA-seq datasets can require lots of time and computing resources to analyze * Generation of raw RNA-seq reads, as opposed to alignments or transcript-level abundance estimates * Transparency/open-source code

Proper citation: Polyester (RRID:SCR_003602) Copy   

•   Source: SciCrunch Registry

http://sing.ei.uvigo.es/GC/

Tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification. While the user can work with different gene set collections and several microarray data files to configure specific classification experiments, the tool is able to run several tests in parallel. It is able to render valuable information for diagnostic analyses and clinical management decisions based on systematically evaluating custom hypothesis over different data sets using complementary classifiers, a key aspect in clinical research.

Proper citation: GeneCommittee (RRID:SCR_004168) Copy   

•   Source: SciCrunch Registry

http://taylorlab.ucsf.edu/software_data.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documentedt on January 10, 2023. Software that implements babel routines for identifying unusual ribosome protected fragment counts given mRNA counts, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Babel (RRID:SCR_004307) Copy   

•   Source: SciCrunch Registry

http://www.egappreviews.org/

Initiative to develop a systematic, evidence-based process for evaluating genetic tests and other applications of genomic technology that are rapidly moving from research to use in clinical practice. A key objective of this process is to provide objective, timely, and credible information that is clearly linked to the scientific evidence on specific applications of genetic and genomic tests. The primary focus of EGAPP activities is an independent, nonfederal expert panel, the EGAPP Working Group. Other components of the EGAPP initiative include a federal interagency, the CDC staff and consultants, and an EGAPP initiative evaluation team.

Proper citation: EGAPP (RRID:SCR_004189) Copy   

•   Source: SciCrunch Registry

http://kwanlab.bio.cuhk.edu.hk/BSRD/

A repository for bacterial small regulatory RNA. They welcome you to submit new experimental validated sRNA targets.

Proper citation: BSRD (RRID:SCR_004249) Copy   

•   Source: SciCrunch Registry