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https://github.com/MikkelSchubert/paleomix

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software toolkit for the processing of ancient and modern HTS data. PALEOMIX also aids in metagenomic analysis of the extracts from the HTS processing.

Proper citation: PALEOMIX (RRID:SCR_015057) Copy   

•   Source: SciCrunch Registry

http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula

Software tool developed for automatically reconstructing a set of major white matter pathways in the brain from diffusion weighted images using probabilistic tractography. This method utilizes prior information on the anatomy of the pathways from a set of training subjects. By incorporating this prior knowledge in the reconstruction procedure, our method obviates the need for manual intervention with the tract solutions at a later stage and thus facilitates the application of tractography to large studies. The trac-all script is used to preprocess raw diffusion data (correcting for eddy current distortion and B0 field inhomogenities), register them to common spaces, model and reconstruct major white matter pathways (included in the atlas) without any manual intervention. trac-all may be used to execute all the above steps or parts of it depending on the dataset and user''''s preference for analyzing diffusion data. Alternatively, scripts exist to execute chunks of each processing pipeline, and individual commands may be run to execute a single processing step. To explore all the options in running trac-all please refer to the trac-all wiki. In order to use this script to reconstruct tracts in Diffusion images, all the subjects in the dataset must have Freesurfer Recons.

Proper citation: TRACULA (RRID:SCR_013152) Copy   

•   Source: SciCrunch Registry

http://www.omicsdi.org/

Portal for dataset discovery across a heterogeneous, distributed group of transcriptomics, genomics, proteomics and metabolomics data resources. These resources span eight repositories in three continents and six organisations, including both open and controlled access data resources.

Proper citation: Omics Discovery Index (RRID:SCR_010494) Copy   

•   Source: SciCrunch Registry

http://doa.nubic.northwestern.edu/pages/search.php

Project portal for a collaborative database aiming to provide a comprehensive annotation to human genome.It uses the computable, controlled vocabulary of Disease Ontology (DO) and NCBI Gene Reference Into Function (GeneRIF).

Proper citation: DOAF (RRID:SCR_015666) Copy   

•   Source: SciCrunch Registry

http://subread.sourceforge.net/

Software package for high-performance read alignment, quantification and mutation discovery.General purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. Subread aligner as fast, accurate and scalable read mapping by seed-and-vote.These programs were also implemented in Bioconductor R package Rsubread.

Proper citation: Subread (RRID:SCR_009803) Copy   

•   Source: SciCrunch Registry

http://www.rhino3d.com/features

3D modeling software used to create, edit, analyze, document, render, animate, and translate surfaces, solids, point clouds, and polygon meshes. It can also be used to analyze and manufacture a variety of products.

Proper citation: Rhinoceros (RRID:SCR_014339) Copy   

•   Source: SciCrunch Registry

https://github.com/eead-csic-compbio/split_pairs

Software for processing NGS sequence reads in FASTQ and FASTA formats. split_pairs.pl is suited particularly for the task of sorting pair end reads and for modifying their headers with Perl-style regular expressions.

Proper citation: split_pairs.pl (RRID:SCR_015707) Copy   

•   Source: SciCrunch Registry

http://dayhoff.anu.edu.au/

It is part of the Institute for Advanced Studies at The Australian National University (ANU). CBiS forms a bridge between two areas of major strength at ANU, mathematics and biological sciences. CBiS brings together researchers with backgrounds in mathematics, statistics and quantitative biology with the goal of developing a conceptual architecture for an information-based, integrative approach to complex biological systems. Software available for download or use is: * Pozitiv * GE Bi-Plot * Chip Stability * PyEvolve * Vestige Most software is freely available under the GPL or similar licenses. For details, see each individual package., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CBiS (RRID:SCR_013408) Copy   

•   Source: SciCrunch Registry

http://www.neuro.uestc.edu.cn/NIT.html

A toolkit for EEG-fMRI multimodal fusion and fMRI data preprocessing and analysis. NIT allows users to perform batch processing of fMRI data analysis and data preprocessing based on SPM8, as well as parallel computing for data preprocessing, nuisance signals removal, and FCD and FOCA calculating. Users can also use NIT to calculate functional connectivity density and four dimensional (spatio-temporal) consistency of local neural activities.

Proper citation: Neuroscience Information Toolbox (RRID:SCR_014501) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/intact/complex/#annotations:fIzBXhJPEeej78Pl6R0ScA

Database and encyclopaedic resource of macromolecular complexes found in key model organisms from scientific literature. Data includes protein-only complexes, protein-small molecules, and protein-nucleic acid complexes. The information within the portal is manually curated and available for download.

Proper citation: Complex Portal (RRID:SCR_015038) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/caworks

A software application developed to support computational anatomy and shape analysis. The capabilities of CAWorks include: interactive landmark placement to create segmentation (mask) of desired region of interest; specialized landmark placement plugins for subcortical structures such as hippocampus and amygdala; support for multiple Medical Imaging data formats, such as Nifti, Analyze, Freesurfer, DICOM and landmark data; Quadra Planar view visualization; and shape analysis plugin modules, such as Large Deformation Diffeomorphic Metric Mapping (LDDMM). Specific plugins are available for landmark placement of the hippocampus, amygdala and entorhinal cortex regions, as well as a browser plugin module for the Extensible Neuroimaging Archive Toolkit.

Proper citation: CAWorks (RRID:SCR_014185) Copy   

•   Source: SciCrunch Registry

http://dsi-studio.labsolver.org

A software for diffusion MR images analysis. The provided functions include reconstruction (DTI, QBI, DSI, and GQI), deterministic fiber tracking, and 3D visualization. It has a window-based interface and operates on Microsoft Windows system.

Proper citation: DSI Studio (RRID:SCR_009557) Copy   

•   Source: SciCrunch Registry

http://rfmri.org/dpabi

Software toolbox for data processing and analysis of brain imaging, evolved from DPARSF (Data Processing Assistant for Resting-State fMRI).

Proper citation: DPABI (RRID:SCR_010501) Copy   

•   Source: SciCrunch Registry

http://asipro.software.informer.com/

An image analysis software.

Proper citation: ASIPro (RRID:SCR_014547) Copy   

•   Source: SciCrunch Registry

http://www.tissuegnostics.com/en/products/analysing-software/tissuequest

Image analysis software for cells and stained areas in samples stained with immunofluorescent markers.

Proper citation: TissueQuest Analysis Software (RRID:SCR_014822) Copy   

•   Source: SciCrunch Registry

http://www.mcid.co.uk/Software/MCID_Analysis

Software designed to provide an image analysis software solution for offline analysis of images, ideally for the analysis of images where image capture is not required. Available applications for MCID Analysis include gel/blot analysis, fluorescence microscopy, and stereology.

Proper citation: MCID Analysis (RRID:SCR_014278) Copy   

•   Source: SciCrunch Registry

https://github.com/cukie/SMIA

Software used to analyze and quantify images stained with multiple fluorophores in vitro or in vivo. It can output both image and value outputs.

Proper citation: SMIA-CUKIE (RRID:SCR_014795) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/erppcatoolkit/

This Matlab toolkit is a general purpose tool for editing, visualizing, and analyzing EEG data (both Event Related Potential - ERP and spectral) whose most recent version has been downloaded over 1000 times. Its three chief highlights are: 1) an optimized automatic artifact correction function that includes ICA correction for eye blinks and saccades. 2) Extensive support for easily conducting PCA and ICA through all stages of the procedure, including inspection of reconstituted waveforms and batch ANOVAs. 3) Implementation of robust ANOVAs, including McCarthy-Wood vector test. It has a graphical user interface for point and click usage and comes with an extensive illustrated tutorial. A description of the toolkit was published in Dien (2010) in Journal of Neuroscience Methods. It relies on both internal functions as well as borrowed functions from both EEGlab and FieldTrip.

Proper citation: ERP PCA Toolkit (RRID:SCR_013105) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/gsa-snp/

A tool for the gene-set (or pathway) analysis of a genome-wide association study result. It accepts a genome-wide list of SNPs and their association P-values. It summarizes the SNP P-values into nearby genes. The gene-by-gene summary results are then further summarized by gene-sets such as Gene Ontology, KEGG pathways, or user-created gene-sets. Various standardization and statistical tests can be performed and the resulting gene-sets that pass a significance level after multiple-testing correction are reported. The tool is written in Java and is available as a standalone version.

Proper citation: GSA-SNP (RRID:SCR_013109) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

Software tool to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files for directional, non-directional or paired-end sequencing. Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for Reduced Representation Bisulfite Sequencing data.

Proper citation: Trim Galore (RRID:SCR_011847) Copy   

•   Source: SciCrunch Registry