Tools   Select Another Resource Report Type

http://www.phidot.org/software/mark/background/

Software tool to provide parameter estimates from marked animals when they are re-encountered at later time, to create population size estimates. Used for analysis of data from marked individuals.

Proper citation: Program MARK (RRID:SCR_019281) Copy   

•   Source: SciCrunch Registry

https://github.com/sciensic/SCIGA

Software Perl toolkit for 10X single cell immunoglobulin repertoires analysis. Uses raw reads or output of Cellranger as input and performs reads quality control, immunoglobulin sequence assembly, sequence annotation, heavy- and light- chain pairing, computing statistics and visualizing.

Proper citation: SCIGA (RRID:SCR_021002) Copy   

•   Source: SciCrunch Registry

http://api.brain-map.org/api/v2/structure_graph_download/1.json

Developed for Allen Reference Atlas and follows terminology from Brain Maps: Structure for the Rat Brain (Swanson, 2004, 2018). The ontology has been subsequently extended and revised to also serve as structure ontology for Allen Mouse Common Coordinate Framework.Defines hierarchical partonomy of anatomical structures of adult mouse brain. At top level, brain is divided into gray matter, fiber tracts and ventricular systems. Gray matter is subdivided into cerebrum, brain stem, and cerebellum, which are themselves organized into subregions in hierarchical tree.

Proper citation: Allen Mouse Reference Atlas Ontology (RRID:SCR_021000) Copy   

•   Source: SciCrunch Registry

https://www.miltenyibiotec.com/products/macs-flow-cytometry/software/flowlogic-software.html

Software tool for flow cytometry data analysis by Miltenyi Biotec.

Proper citation: Flowlogic (RRID:SCR_020942) Copy   

•   Source: SciCrunch Registry

https://www.brainlatam.com/knowledge-base/brainvision-pycorder-installation-262

Open source acquisition program, based on Python programming language, for setting up BrainVision actiCHamp amplifier and storing data.

Proper citation: BrainVision PyCorder (RRID:SCR_019286) Copy   

•   Source: SciCrunch Registry

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

Software R package for power analysis of generalized linear mixed models by simulation. Used to calculate power for generalised linear mixed models.

Proper citation: SIMR (RRID:SCR_019287) Copy   

•   Source: SciCrunch Registry

https://sydneybiox.github.io/CiteFuse/

Software R package consisting of suite of tools for doublet detection, modality integration, clustering, differential RNA and protein expression analysis, antibody-derived tag evaluation, ligand-receptor interaction analysis and interactive web-based visualization of CITE-seq data.

Proper citation: CiteFuse (RRID:SCR_019321) Copy   

•   Source: SciCrunch Registry

https://guoweilong.github.io/BS_Seeker2/index.html

Software tool as versatile aligning pipeline for bisulfite sequencing data. Used for mapping bisulfite sequencing data and generating DNA methylomes. Improves mappability over existing aligners by using local alignment. Maps reads from RRBS library by building special indexes with improved efficiency and accuracy. Provides additional function for filtering out reads with incomplete bisulfite conversion, which is useful in minimizing overestimation of DNA methylation levels.

Proper citation: Bs-Seeker2 (RRID:SCR_020948) Copy   

•   Source: SciCrunch Registry

https://labsn.github.io/expyfun/index.html

Auditory and visual stimulus delivery library for psychoacoustics in Python.

Proper citation: Expyfun (RRID:SCR_019285) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3001096/

Software pipeline to identify MITEs as well as other small Class 2 non autonomous Transposable Elements from genomic DNA data sets. Used for discovering miniature inverted repeat transposable elements from genomic sequences. Can search large genomic data sets including whole genome sequences.

Proper citation: MITE-Hunter (RRID:SCR_020946) Copy   

•   Source: SciCrunch Registry

https://qiwei.shinyapps.io/PredictCOVID19/

Web app to help assess both short- and long-term forecasts of COVID-19 across the United States at multiple levels. Done by implementing one time-series model (ARIMA), one compartmental models (basic SIR), and six classical growth models, which all yield satisfactory prediction results in the past and current pandemics at early stage.

Proper citation: BayesEpiModels Web App (RRID:SCR_019292) Copy   

•   Source: SciCrunch Registry

http://crosslinkviewer.org/

Open source web based visualization tool for exploring crosslinking mass spectrometry results. Displays residue resolution positional information including linkage sites and linked peptides, all types of crosslinking reaction product, ambiguous results and additional sequence information such as domains.

Proper citation: xiNET (RRID:SCR_021010) Copy   

•   Source: SciCrunch Registry

https://biofactoid.org

Web tool for creating digital profile of scientific discoveries in article and connecting them to related research. Authors describe molecular interactions supported by their results, letting researchers explore first hand account of article findings and connect to related articles and knowledge. Web based system for scientists to compose structured representation of networks of interactions between genes, their products, and chemical compounds, represented using power of formal ontology.

Proper citation: Biofactoid (RRID:SCR_021011) Copy   

•   Source: SciCrunch Registry

https://cgmaptools.github.io

Software package for DNA methylation analysis. Used for context-wise, gene-wise, bin-wise, region-wise and sample-wise analysis and visualizations. Used to improve precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data.

Proper citation: cgmapotools (RRID:SCR_020950) Copy   

•   Source: SciCrunch Registry

https://immuneml.uio.no/

Open source Python platform for machine learning based analysis and classification of adaptive immune receptors and repertoires. Supported by ELIXIR Norway.

Proper citation: immuneML (RRID:SCR_021004) Copy   

•   Source: SciCrunch Registry

https://huggingface.co

Portal to build, train and deploy state of the art models powered by reference open source in natural language processing.

Proper citation: Hugging Face (RRID:SCR_020958) Copy   

•   Source: SciCrunch Registry

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

Software R package as collection of functions to create spatial weights matrix objects from polygon contiguities, from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree.

Proper citation: spdep (RRID:SCR_019294) Copy   

•   Source: SciCrunch Registry

https://github.com/Niinleslie/MesKit

Software R package for dissecting cancer evolution from multi region derived tumor biopsies via somatic mutations. Used for characterizing cancer genomic ITH and inferring history of tumor evolution via implementation of well established computational and statistical methods.

Proper citation: MesKit (RRID:SCR_020959) Copy   

•   Source: SciCrunch Registry

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

Software R package as scale functions for visualization. Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends.

Proper citation: scales (RRID:SCR_019295) Copy   

•   Source: SciCrunch Registry

https://exrna-atlas.org

Software tool as data and metadata repository of Extracellular RNA Communication Consortium. Atlas includes small RNA sequencing and qPCR derived exRNA profiles from human and mouse biofluids. All RNAseq datasets are processed using version 4 of exceRpt small RNAseq pipeline. Atlas accepts submissions for RNAseq or qPCR data.

Proper citation: exRNA Atlas (RRID:SCR_017221) Copy   

•   Source: SciCrunch Registry