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http://www.nitrc.org/projects/inia19/

Primate brain atlas created from over 100 structural MR scans of 19 rhesus macaque animals. The atlas currently comprises high-resolution T1-weighted average MR images with and without skull stripping, tissue probability maps, and a detailed parcellation map based on the NeuroMaps atlas.

Proper citation: INIA19 Primate Brain Atlas (RRID:SCR_009498) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/r-spit/

Group ICA (Independent Component Analysis) was used to generate spatial templates for 12 common resting-state networks in 62 typically-developing children, ages 9-15. They have made these available for those that will find them useful for masking and spatial template matching procedures. Basic demographic data on the sample is provided along with the protocol used to generate the templates.

Proper citation: resting-state pediatric imaging template (RRID:SCR_009647) Copy   

•   Source: SciCrunch Registry

http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009

Unbiased standard magnetic resonance imaging template brain volume for normal population. These volumes were created using data from ICBM project. 6 different templates are available: * ICBM 2009a Nonlinear Symmetric - template which includes T1w,T2w,PDw modalities, also T2 relaxometry (T2 values calculated for each subject using single dual echo PD/T2 scan), and tissue probabilities maps. Also included lobe atlas used for ANIMAL+INSECT segmentation, brain mask, eye mask and face mask. Intensity inhomogeneity was performed using N3 version 1.10.1. * ICBM 2009a Nonlinear Asymmetric template - template which includes T1w,T2w,PDw modalities, and tissue probabilities maps. Intensity inhomogeneity was performed using N3 version 1.10.1. Also included brain mask, eye mask and face mask. * ICBM 2009b Nonlinear Symmetric - template which includes only T1w,T2w and PDw modalities. * ICBM 2009b Nonlinear Asymmetric - template which includes only T1w,T2w and PDw modalities. * ICBM 2009c Nonlinear Symmetric - template which includes T1w,T2w,PDw modalities, and tissue probabilities maps. Also included lobe atlas used for ANIMAL+INSECT segmentation, brain mask, eye mask and face mask. Intensity inhomogeneity was performed using N3 version 1.11. Sampling is different from 2009a template. * ICBM 2009c Nonlinear Asymmetric template - template which includes T1w,T2w,PDw modalities, and tissue probabilities maps. Intensity inhomogeneity was performed using N3 version 1.11 Also included brain mask, eye mask and face mask.Sampling is different from 2009a template. All templates are describing the same anatomy, but sampling is different. Also, different versions of N3 algorithm produces slightly different tissue probability maps. Tools for using these atlases can be found in the Software section. Viewing the multiple atlas volumes online requires Java browser support. You may also download the templates - see licensing information.

Proper citation: ICBM 152 Nonlinear atlases version 2009 (RRID:SCR_008796) Copy   

•   Source: SciCrunch Registry

http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1

An unbiased standard magnetic resonance imaging template brain volume for pediatric data from the 4.5 to 18.5y age range. These volumes were created using data from 324 children enrolled in the NIH-funded MRI study of normal brain development (Almli et al., 2007, Evans and Group 2006). Tools for using these atlases can be found in the Software section. To view the atlases online, click on the appropriate JIV2 link in the Download section. You can download templates constructed for different age ranges. For each age range you will get an average T1w, T2w, PDw maps normalized between 0 and 100 and tissue probability maps, with values between 0 and 1. Also each age range includes a binary brain mask.

Proper citation: NIHPD Objective 1 atlases (4.5 - 18.5y) (RRID:SCR_008794) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/ibdreg/index.html

Software package in S-PLUS and R to test genetic linkage with covariates by regression methods with response IBD sharing for relative pairs. Account for correlations of IBD statistics and covariates for relative pairs within the same pedigree. (entry from Genetic Analysis Software)

Proper citation: IBDREG (RRID:SCR_013127) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=GenBinomApps

Software R package as collection of functions to compute the Clopper-Pearson Confidence Interval and the required sample size. Density, distribution function, quantile function and random generation for the Generalized Binomial Distribution.Enhanced model for burn-in studies, where failures are tackled by countermeasures.

Proper citation: GenBiomApps (RRID:SCR_025542) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=km.ci

Software R package to compute various confidence intervals for the Kaplan-Meier estimator, namely: Peto's CI, Rothman CI, CI's based on Greenwood's variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by Nair and Hall and Wellner.

Proper citation: km.ci (RRID:SCR_025543) Copy   

•   Source: SciCrunch Registry

https://kimlab.io/brain-map/DevCCF/

Open access multimodal 3D atlases of developing mouse brain that can be used to integrate mouse brain imaging data for visualization, education, cell census mapping, and more. Atlas ages include E11.5, E13.5, E15.5, E18.5, P4, P14, and P56. Web platform can be utilized to visualize and explore the atlas in 3D. Downloadable atlas can be used to align multimodal mouse brain data. Morphologically averaged symmetric template brains serve as the basis reference space and coordinate system. Anatomical labels are manually drawn in 3D based on the prosomeric model. For additional references, the P56 template includes templates and annotations from the aligned Allen Mouse Brain Common Coordinate Framework (Allen CCFv3) and aligned Molecular Atlas of the Adult Mouse Brain.

Proper citation: 3D Developmental Mouse Brain Common Coordinate Framework (RRID:SCR_025544) Copy   

•   Source: SciCrunch Registry

https://github.com/PacificBiosciences/pbmm2?tab=readme-ov-file

Software application as minimap2 frontend for PacBio native data formats. SMRT C++ wrapper for minimap2's C API.

Proper citation: pbmm2 (RRID:SCR_025549) Copy   

•   Source: SciCrunch Registry

https://github.com/franapoli/signed-ks-test

Software tool as modified R ks.test to obtain sign and force exact p-value.

Proper citation: signed ks test (RRID:SCR_025636) Copy   

•   Source: SciCrunch Registry

https://academic.oup.com/biostatistics/article/23/4/1200/6561796

Software for multi-omic data integration. Used to jointly decompose multiple biologically related experimental data sets with biological and technological relationships that can be structured into the decomposition.

Proper citation: 2s-LCA (RRID:SCR_025613) Copy   

•   Source: SciCrunch Registry

https://academic.oup.com/bioinformatics/article/35/12/2159/5184284

Algorithm for regulatory network inference using gradient boosting, based on GENIE3 architecture. Used for inference of gene regulatory networks.

Proper citation: GRNBoost2 (RRID:SCR_025614) Copy   

•   Source: SciCrunch Registry

https://github.com/Cloud-SPAN

Cloud-based high performance computing for specialised analyses on environmental omics.

Proper citation: Cloud-SPAN (RRID:SCR_025594) Copy   

•   Source: SciCrunch Registry

https://tristanic.github.io/isolde/

Software environment to ease task of building macromolecular models into low to medium resolution experimental maps. Physically realistic environment for model building into low-resolution electron-density maps. Can generate maps directly from crystallographic F/sigF data in MTZ format and automatically re-calculate them when model changes, and/or generate "static" maps from pre-calculated F/phi data.

Proper citation: ISOLDE (RRID:SCR_025577) Copy   

•   Source: SciCrunch Registry

https://camarades.shinyapps.io/ASySD/

Open source, interoperable software tool to remove duplicate citations in biomedical systematic reviews.

Proper citation: Automated Systematic Search Deduplicator (RRID:SCR_025607) Copy   

•   Source: SciCrunch Registry

https://www.vivoquant.com/

Software multi-modality post-processing suite for SPECT, CT, PET, MR, Optical and and Autoradiography imaging data.

Proper citation: Invicro Vivoquant (RRID:SCR_025778) Copy   

•   Source: SciCrunch Registry

https://github.com/EGA-archive/EuCanImage-FHIR

Software application as ETL implementation for EuCanImage, encouraging semantic interoperability of clinical data obtained in studies by transforming it into machine-readable format following FHIR standards. This parser uses FHIR Resources in order to create dictionaries following FHIR compliant structure. Code Language is written in Python 3.11. Outputs are JSON files compliant with FHIR 4.3 schemas.This script is specifically created for the Extract, Transform and Load implementation for EuCanImage, and will follow the structures obtained from the REDCap databases within the study.

Proper citation: EuCanImage FHIR ETL Implementation (RRID:SCR_025824) Copy   

•   Source: SciCrunch Registry

https://seer.cancer.gov/seerstat/

Statistical software for analysis of SEER and other cancer-related databases.Used to view individual cancer records and to produce statistics for studying impact of cancer on population.

Proper citation: SEER*Stat (RRID:SCR_025808) Copy   

•   Source: SciCrunch Registry

https://www.bruker.com/es/products-and-solutions/infrared-and-raman/opus-spectroscopy-software/release-overview.html#accordion-1e89899198-item-06b2720261

Software developed by Bruker for analysis and processing of spectroscopic data. Used for measurement, processing and evaluation of IR, NIR and Raman spectra.

Proper citation: Bruker OPUS (RRID:SCR_025806) Copy   

•   Source: SciCrunch Registry

https://github.com/ratan-lab/sumo

Software for multiomic nonnegative matrix factorization.

Proper citation: Ratan-lab (SUMO) (RRID:SCR_025687) Copy   

•   Source: SciCrunch Registry