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Software application as helper to run command, capture stdout/stderr and details about running.
Proper citation: con/duct (RRID:SCR_025436) Copy
https://github.com/sokrypton/ColabFold
Software application offers accelerated prediction of protein structures and complexes by combining homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. Used for protein folding.
Proper citation: ColabFold (RRID:SCR_025453) Copy
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
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
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
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
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
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
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
Cloud-based high performance computing for specialised analyses on environmental omics.
Proper citation: Cloud-SPAN (RRID:SCR_025594) Copy
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
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
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
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
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
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
https://github.com/ratan-lab/sumo
Software for multiomic nonnegative matrix factorization.
Proper citation: Ratan-lab (SUMO) (RRID:SCR_025687) Copy
https://kimlab.io/brain-map/DevATLAS/
Whole brain developmental map of neuronal circuit maturation. Generated by whole brain spatiotemporal mapping of circuit maturation during early postnatal development. Standard reference for normative developmental trajectory of neuronal circuit maturation, as well as high throughput platform to pinpoint when and where circuit maturation is disrupted in mouse models of neurodevelopmental disorders, such as fragile X syndrome.
Proper citation: DevATLAS (RRID:SCR_025718) Copy
https://github.com/ElemeFE/element-angular
Open-source angularjs theme. Element for Angular.
Proper citation: ElemeFE element-angular (RRID:SCR_025725) Copy
https://pubmed.ncbi.nlm.nih.gov/36123081/
Behavior change intervention software. Participants enter their data as part of online survey, and software generates individualized feedback letters.
Proper citation: PAL:Proactive Automatized Lifestyle intervention (RRID:SCR_025727) Copy
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