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Commercial supplier of antibodies, reagents, and dyes for research.
Proper citation: AnaSpec (RRID:SCR_002114) Copy
http://openmeeg.gforge.inria.fr
A C++ package for low-frequency bio-electromagnetism solving forward problems in the field of EEG and MEG with very high accuracy.
Proper citation: OpenMEEG (RRID:SCR_002510) Copy
http://clip.med.yale.edu/presto/
Software toolkit for processing raw reads from high-throughput sequencing of lymphocyte repertoires.
Proper citation: pRESTO (RRID:SCR_001782) Copy
http://www.crl.med.harvard.edu/software/STAPLE/index.php
An algorithm for the Simultaneous Truth and Performance Level Estimation, which estimates a reference standard and segmentation generator performance from a set of segmentations. It has been widely applied for the validation of image segmentation algorithms, and to compare the performance of different algorithms and experts. It has also found application in the identification of a consensus segmentation, by combination of the output of a group of segmentation algorithms, and for segmentation by registration and template fusion., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: STAPLE (RRID:SCR_002590) Copy
http://www.math.hkbu.edu.hk/~mng/CLUSTAG/CLUSTAG.html
Software application that uses hierarchical clustering and graph methods for selecting tag SNPs (single nucleotide polymorphisms). Cluster and set-cover algorithms are developed to obtain a set of tag SNPs that can represent all the known SNPs in a chromosomal region, subject to the constraint that all SNPs must have a squared correlation R2 > C with at least one tag SNP, where C is specified by the user. The program is implemented with Java, and it can run in Windows platform as well as the Unix environment.
Proper citation: CLUSTAG (RRID:SCR_001816) Copy
A package for writing fMRI analysis pipelines and interfacing with external analysis packages (SPM, FSL, AFNI). Current neuroimaging software offer users an incredible opportunity to analyze their data in different ways, with different underlying assumptions. However, this has resulted in a heterogeneous collection of specialized applications without transparent interoperability or a uniform operating interface. Nipype, an open-source, community-developed initiative under the umbrella of Nipy, is a Python project that solves these issues by providing a uniform interface to existing neuroimaging software and by facilitating interaction between these packages within a single workflow. Nipype provides an environment that encourages interactive exploration of algorithms from different packages (e.g., SPM, FSL), eases the design of workflows within and between packages, and reduces the learning curve necessary to use different packages. Nipype is creating a collaborative platform for neuroimaging software development in a high-level language and addressing limitations of existing pipeline systems.
Proper citation: Nipype (RRID:SCR_002502) Copy
https://community.brain-map.org/t/allen-human-reference-atlas-3d-2020-new/405
Parcellation of adult human brain in 3D, labeling every voxel with brain structure spanning 141 structures. These parcellations were drawn and adapted from prior 2D version of adult human brain atlas.
Proper citation: Allen Human Reference Atlas, 3D, 2020 (RRID:SCR_017764) Copy
http://tools.thermofisher.com/content/sfs/manuals/cms_040970.pdf
Automated PCR instrument for automated amplification of nucleic acids with Polymerase Chain Reaction. It has reaction volumes of up to 50 uL and sample temperature range of 4 to 99.9 C.
Proper citation: Thermo Fisher: Applied Biosystems: GeneAmp 9700 PCR Thermocycler System (RRID:SCR_018436) Copy
https://github.com/ttrogers/DecodingDynamic
Data, code, and notebooks for replicating analyses reported in Rogers et al., Evidence for deep, distributed and dynamic semantic code in human ventral anterior temporal cortex.
Proper citation: DecodingDynamic (RRID:SCR_021099) Copy
https://kimlab.io/brain-map/atlas/
Labels provide resource to isolate and identify mouse brain anatomical structures. Cell type specific transgenic mice and an MRI atlas were used to adjust and further segment the labels. Highly segmented anatomical labels in the adult mouse brain common coordinate framework.
Proper citation: Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas (RRID:SCR_022816) Copy
https://drive.google.com/drive/folders/1K5oiXPcZDPT40irrZ_G2hZ86uNGA7CYZ?usp=sharing
Reference atlas for mice. Contains both average and annotation templates.
Proper citation: fMOST Atlas (RRID:SCR_022868) Copy
https://metacpan.org/dist/Bio-EUtilities
Software package which interacts with and retrieves data from NCBI's eUtils. This distribution encompasses low-level API for interacting with (and storing) information from NCBI's eUtils interface. See Bio::DB::EUtilities for the query API to retrieve data from NCBI, and Bio::Tools::EUtilities for the general class storage system. Note this may change to utilize the XML schema for each class at some point, though we will attempt to retain current functionality for backward compatibility unless this becomes problematic.
Proper citation: Bio-EUtilities (RRID:SCR_024064) Copy
https://metacpan.org/dist/Bio-Tools-Run-Alignment-Clustalw
Software package for performing multiple sequence alignment from set of unaligned sequences and/or sub-alignments by means of the clustalw program.
Proper citation: Bio-Tools-Run-Alignment-Clustalw (RRID:SCR_024067) Copy
https://metacpan.org/dist/Bio-Tools-Phylo-PAML
Software package used to parse output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00. You can use the Bio-Tools-Run-Phylo-PAML modules to actually run some of the PAML programs, but this module is only useful to parse the output.
Proper citation: Bio-Tools-Phylo-PAML (RRID:SCR_024069) Copy
https://metacpan.org/dist/Bio-Graphics
Software package to generate GD images of Bio::Seq objects.
Proper citation: Bio-Graphics (RRID:SCR_024061) Copy
https://github.com/genouest/biomaj-cli
Software package to use BioMAJ providing biomaj-cli.
Proper citation: CLI for BioMAJ (RRID:SCR_023980) Copy
Software pipeline for taxonomic classification of contigs and metagenome-assembled genomes. Contig Annotation Tool and Bin Annotation Tool for the taxonomic classification of long DNA sequences and metagenome assembled genomes of both known and unknown microorganisms, as generated by contemporary metagenomics studies.
Proper citation: CAT and BAT (RRID:SCR_023988) Copy
https://github.com/mroosmalen/nanosv
Software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies� MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers.
Proper citation: NanoSV (RRID:SCR_024127) Copy
https://github.com/bioinfo-ut/GenomeTester4
Software toolkit for performing set operations - union, intersection and complement on k-mer lists.
Proper citation: GenomeTester4 (RRID:SCR_024026) Copy
https://github.com/nextstrain/augur
Software package to track evolution from sequence and serological data. Provides collection of commands which are designed to be composable into larger processing pipelines.
Proper citation: Augur (RRID:SCR_023964) Copy
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