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https://github.com/WGS-TB/MentaLiST
Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes.
Proper citation: MentaLiST (RRID:SCR_016469) Copy
Software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.
Proper citation: cisTEM (RRID:SCR_016502) Copy
http://www.indecbiosystems.com/imagingworkbench/default.asp
Software for multichannel dynamic fluorescence image acquisition and analysis by INDEC BioSystems.
Proper citation: Imaging WorkBench (RRID:SCR_016589) Copy
https://www.mrc-lmb.cam.ac.uk/kzhang/Gctf/
Software tool as a Graphics Processing Units (GPU) accelerated computer program for real-time contrast transfer function (CTF) determination and correction. Used for a near-atomic resolution cryo electron microscopy (cryoEM) reconstruction to maximize the cross-correlation of a simulated CTF with the logarithmic amplitude spectra (LAS) of observed micrographs after background subtraction., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: GCTF (RRID:SCR_016500) Copy
https://sleepdata.org/datasets/bestair/
Portal for sleep study to address challenges in conducting future large-scale trials of sleep apnea treatment. Includes data from sleep apnea patients with cardiovascular disease or risk factors. Signals included in the polysomnography (PSG) montage are ECG, SpO2, airflow, nasal pressure, position, pulse, respiratory effort, snore, tidal volume.
Proper citation: Best Apnea Interventions for Research (BestAIR) sleep study (RRID:SCR_016583) Copy
https://pachterlab.github.io/kallisto/about
Software tool for quantifying abundances of transcripts from RNA-Seq data or target sequences using high-throughput sequencing reads.
Proper citation: kallisto (RRID:SCR_016582) Copy
https://imaps.genialis.com/iclip
Web server for analysis of high-resolution sequencing data. It can be used with all variants of CLIP,as well as with methods that interrogate RNA or DNA methylation, RNA processing, RNA structure or protein-DNA interactions.
Proper citation: iMaps (RRID:SCR_016705) Copy
https://github.com/fbreitwieser/pavian
Software R package for interactive analysis of metagenomics classification results with a special focus on infectious disease diagnosis. Used for analyzing and visualization of metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Provides an alignment viewer for validation of matches to a particular genome.
Proper citation: Pavian (RRID:SCR_016679) Copy
https://github.com/tomazc/iCount
Software Python package for protein-RNA interaction analysis. Used for analysis of protein-RNA interactions with iCLIP sequencing data and RNA maps.
Proper citation: iCount (RRID:SCR_016712) Copy
https://github.com/umerijaz/nanopore
Software for a workflow for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform. Used for full-length SSU rRNA gene sequencing.
Proper citation: NanoAmpli-Seq (RRID:SCR_016710) 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://biophysics.fsu.edu/facilities/physical-biochemistry-facility/
Facility for biophysical studies of macromolecules with emphasis on providing resources, instrumentation, training, and guidance to graduate and undergraduate students.
Proper citation: Florida State University Physical Biochemistry Core Facility (RRID:SCR_016714) Copy
Software to provide control of the cell sorter from configuration and compensation setup to acquisition, sorting, and analysis, making it easy to customize the instrument for specific applications. BD implements software solutions that integrate data, devices and systems.
Proper citation: BD FACS Sortware sorter software (RRID:SCR_016722) Copy
Collection of disease maps, and mapped collection data and distribution models for arthropod disease vector species, including mosquitoes, ticks, sand flies, mites, and fleas, as well as the hosts/reservoirs of vector-borne disease pathogens. VectorMap is modeled after MosquitoMap.
Proper citation: VectorMap (RRID:SCR_016721) 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
ImageJ plug-in to quantify fibrillar structures in raw microscopy images. Used to evaluate the orientation of fiber orientation pattern and plots the results in the image.
Proper citation: FibrilTool (RRID:SCR_016773) Copy
https://github.com/ToolsVanBox/smMIPfil
Software tool for single molecule Molecular Inversion Probes data analysis. This is a stand-alone perl script. Except that this is dependent on the samtools, no installation required.
Proper citation: smMIPfil (RRID:SCR_016892) Copy
https://github.com/zitmen/thunderstorm
Software tool for automated processing, analysis, and visualization of data acquired by single molecule localization microscopy methods such as PALM and STORM. ImageJ interactive and modular plugin for SMLM data analysis and super-resolution imaging.
Proper citation: Thunder STORM (RRID:SCR_016897) Copy
Software tool for multi level analysis of applications optimized for ImageXpress instruments. High-content image analysis software featuring time lapse analysis. Used for 2D and 3D imaging.
Proper citation: MetaXpress (RRID:SCR_016654) Copy
https://crispr.cos.uni-heidelberg.de/
Web tool for CRISPR/Cas9 target prediction. Identifies and ranks all candidate sgRNA target sites according to their off-target quality and displays full documentation.
Proper citation: CCTop (RRID:SCR_016890) Copy
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