Tools   Select Another Resource Report Type

https://bioconductor.org/packages/release/bioc/html/apeglm.html

Software package provides Bayesian shrinkage estimators for effect sizes for variety of GLM models, using approximation of posterior for individual coefficients.

Proper citation: apeglm (RRID:SCR_026951) Copy   

•   Source: SciCrunch Registry

https://github.com/PathoGenOmics-Lab/VIPERA

Software package to automate analysis of evolutionary trajectories over time of series of sequences from same viral infection. Snakemake workflow for SARS-CoV-2 viral intra-patient evolution reporting and analysis.

Proper citation: VIPERA (RRID:SCR_026964) Copy   

•   Source: SciCrunch Registry

https://github.com/lvrgb777/STPoseNet

Source code for pose recognition model for laboratory mice based on yolov8. Real-time spatiotemporal network model for robust mouse pose estimation.

Proper citation: STPoseNet (RRID:SCR_026834) Copy   

•   Source: SciCrunch Registry

https://jnm.snmjournals.org/content/46/6/1023.long

Software to evaluate mean absorbed doses to organs and tumors in radionuclide images, providing simple and fast solution for radionuclide imaging and treatment of new drugs in clinical trials. Calculates radiation doses to organs and the whole body based on established human body models.

Proper citation: OLINDA/EXM (RRID:SCR_026835) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/tguenther/read/src/master/

Software tool to infer family relationships for degraded samples. Used to infer degree of relationship (up to second degree, i.e. nephew/niece-uncle/aunt, grandparent-grandchild or half-siblings) for pair of low-coverage individuals.

Proper citation: READ (RRID:SCR_026958) Copy   

•   Source: SciCrunch Registry

https://www.dotmatics.com/capabilities/electronic-lab-notebook

Software for scientific research and development. ELN captures and manages experimental data, while Data Discovery Platform enables users to explore, analyze, and visualize that data to gain insights.

Proper citation: Dotmatics ELN and Data Discovery Platform (RRID:SCR_027029) Copy   

•   Source: SciCrunch Registry

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

Software R package used in survival analysis that evaluates predictive accuracy of survival model. Measures how well model can distinguish between pairs of individuals with different survival times. Calculates proportion of all pairs of individuals whose predicted survival times are correctly ordered.

Proper citation: Concordance Probability Estimates (RRID:SCR_027140) Copy   

•   Source: SciCrunch Registry

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

Software R package to perform fixed and random-effects multivariate and univariate meta-analysis and meta-regression.

Proper citation: mvmeta (RRID:SCR_027142) Copy   

•   Source: SciCrunch Registry

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

Software R package for estimation of causal mediation effects. Allows researchers to conduct sensitivity analysis for certain parametric models.

Proper citation: mediation (RRID:SCR_026984) Copy   

•   Source: SciCrunch Registry

http://www.atgc-montpellier.fr/permutmatrix/

Software package for analysing and visualising data. Graphical environment to arrange gene expression profiles in optimal linear order.

Proper citation: PermutMatrix (RRID:SCR_026979) Copy   

•   Source: SciCrunch Registry

https://github.com/fmaureira/ArguelloALab

Software repository contains protocol for video acquisition and pose estimation analysis using DeepLabCut and Simple Behavioral Analysis.

Proper citation: Analysis of Operant Self-administration Behaviors with Supervised Machine Learning (RRID:SCR_027003) Copy   

•   Source: SciCrunch Registry

https://github.com/mskilab-org/JaBbA

Software tool to infer junction-balanced genome graphs with high fidelity. Builds genome graph based on junctions and read depth from whole genome sequencing, inferring optimal copy numbers for both vertices (DNA segments) and edges (bonds between segments).

Proper citation: JaBba (RRID:SCR_027134) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/anthakki/prism/src/master/

Software statistical framework that allows simultaneous extraction of tumor sample composition and cell type and sample specific whole-transcriptome profiles from individual bulk RNA-seq samples.

Proper citation: PRISM - Poisson RNA-profile Identification in Scaled Mixtures (RRID:SCR_027136) Copy   

•   Source: SciCrunch Registry

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

Software R package for analysis and visualization of macroevolutionary dynamics on phylogenetic trees.

Proper citation: BAMMtools (RRID:SCR_027137) Copy   

•   Source: SciCrunch Registry

https://www.sbg.bio.ic.ac.uk/docking/ftdock.html

Software tool to discrete two molecules onto orthogonal grids and performs global scan of translational and rotational space.

Proper citation: FTDock (RRID:SCR_027019) Copy   

•   Source: SciCrunch Registry

https://github.com/hartwigmedical/hmftools/tree/master/cobalt

Software tool to determine read depth ratios of supplied tumor and reference genomes.

Proper citation: COBALT (RRID:SCR_027132) Copy   

•   Source: SciCrunch Registry

https://www.ethotrack.com/fr/

Video analysis software designed for the study of animal behavior.

Proper citation: Ethotrack (RRID:SCR_027105) Copy   

•   Source: SciCrunch Registry

https://github.com/gillislab/MetaMarkers

Software R package to efficiently compute robust markers across single-cell datasets. Robust marker signatures from single-cell data.

Proper citation: MetaMarkers (RRID:SCR_027104) Copy   

•   Source: SciCrunch Registry

https://caravagnalab.github.io/CNAqc/

Software package to quality control bulk cancer sequencing data. Used to visualise and manipulate i) somatic mutation data of both single-nucleotide variants and insertion-deletions, ii) allele-specific Copy Number Alterations (CNAs) and iii) tumour purity estimates. Used to validate copy number segmentations against variant allele frequencies of somatic mutations. Provides automatic copy number calling pipeline. Provides also algorithms to phase mutation multiplicities against CNAs and estimate Cancer Cell Fractions (CCFs) with their uncertainty.

Proper citation: CNAqc (RRID:SCR_027066) Copy   

•   Source: SciCrunch Registry

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

Software R package to convert between human and non-human gene orthologs/homologs. Integrates orthology assertion predictions sourced from multiple databases as compiled by the HGNC Comparison of Orthology Predictions (HCOP) (Wright et al. 2005 , Eyre et al. 2007 , Seal et al. 2011 ).

Proper citation: babelgene (RRID:SCR_027117) Copy   

•   Source: SciCrunch Registry