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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MSM Resource Report Resource Website 1+ mentions |
MSM (RRID:SCR_015500) | source code, software resource | Source code for fitting continuous-time Markov and hidden Markov multi-state models to longitudinal data. It was originally designed for processes observed at arbitrary times in continuous time but some other observation schemes are supported. Both Markov transition rates and the hidden Markov output process can be modelled in terms of covariates, which may be constant or piecewise-constant in time. | markov, continuous time markov, hidden markov multi state model | is hosted by: CRAN | DOI:10.18637/jss.v038.i08 | Available for download | https://www.jstatsoft.org/article/view/v038i08 | SCR_015500 | Multi-State Markov and Hidden Markov Models in Continuous Time (MSM), Multi-State Markov and Hidden Markov Models in Continuous Time | 2026-08-09 09:06:53 | 1 | |||||||
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phytools Resource Report Resource Website 500+ mentions |
phytools (RRID:SCR_015502) | source code, software resource | Software R package for phylogenetic comparative biology. The package contains various functions for phylogenetic analysis of comparative data from species. | r package, phylogenetic comparison, phylogenetic analysis |
is listed by: Debian is listed by: OMICtools is hosted by: GitHub |
DOI:10.1111/j.2041-210X.2011.00169.x | Available for download, Acknowledgement requested | OMICS_12499 | https://github.com/liamrevell/phytools, https://sources.debian.org/src/r-cran-phytools/ | SCR_015502 | 2026-08-09 09:06:41 | 718 | |||||||
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Mikado Resource Report Resource Website 50+ mentions |
Mikado (RRID:SCR_016159) | source code, software resource | Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data * and to select the best models in each locus. | annotation, rna-seq, genomics, transcriptomics | is related to: Portcullis | BBSRC BB/J004669/1; BBSRC BB/J010375/1; BBSRC BB/CSP17270/1; BBSRC BB/CCG1720/1 |
DOI:10.1101/216994 | Free, Available for download | http://mikado.readthedocs.io/ | SCR_016159 | 2026-08-09 09:06:59 | 93 | |||||||
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CUDAICA Resource Report Resource Website 1+ mentions |
CUDAICA (RRID:SCR_015630) | source code, software resource | Software that implements Infomax ICA, which is an algorithm to perform Independent Component Analysis, in CUDA (a parallel computing platform and programming model). | infomax ica, ica, independent component analysis, eeg | PMID:22811699 | Free, Available for download | https://liaa.dc.uba.ar/node/10 | SCR_015630 | 2026-08-09 09:06:27 | 3 | |||||||||
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regist custom genome Resource Report Resource Website 1+ mentions |
regist custom genome (RRID:SCR_015999) | source code, software resource | One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide.. Regist custom genome software registers custom genomes to Genome Explorer (IN: FASTA). | analysis, pipeline, maser, genome, explorer, fasta, custom, register | Ministry of Education ; Culture ; Sports ; Science and Technology ; Japan |
Restricted | http://cell-innovation.nig.ac.jp/maser_cgi/cip-pl_list_violin_en.cgi | SCR_015999 | Management and Analysis System for Enormous Reads: regist custom genome | 2026-08-09 09:06:33 | 1 | ||||||||
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kCSD-python Resource Report Resource Website 1+ mentions |
kCSD-python (RRID:SCR_015777) | source code, software resource | Source code for the Python implementation of the kernel Current Source Density method. The method operates in one-, two-, and three-dimensional space to perform nonparametric estimation of transmembrane current sources from local field potentials recorded from arbitrarily distributed electrodes. | kernel current source density, 1d, 2d, 3d, python, local field potential, transmembrane current source | uses: Python Programming Language | PMID:22091662 | Free, Available for download | SCR_015777 | kernel current source density method - python, kCSD inverse method, Kernel Current Source Density Method | 2026-08-09 09:06:29 | 7 | ||||||||
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lme4 Resource Report Resource Website 100+ mentions |
lme4 (RRID:SCR_015654) | source code, software resource | Software R package. Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue." | linear mixed-effects model, s4 class, eigen c++ library, r package, r, bio.tools |
is listed by: CRAN is listed by: bio.tools is listed by: Debian works with: R package: lmerTest |
Free, Available for download | biotools:lme4 | https://cran.r-project.org/package=lme4, https://github.com/lme4/lme4/, https://bio.tools/lme4 | SCR_015654 | lme4, lme4.0, lme4: Linear Mixed-Effects Models using 'Eigen' and S4, lme4: Linear Mixed-Effects Models, R package: lme4 | 2026-08-09 09:06:54 | 411 | |||||||
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PythonVideoAnnotator Resource Report Resource Website 1+ mentions |
PythonVideoAnnotator (RRID:SCR_025868) | software application, software resource | Software graphical application written in Python, to analyze videos and create notes for events in the video. Used to identify animals’ behaviors based on information extracted from video. | graphical application, analyze videos, create notes, identify animals’ behaviors, | Free, Freely available | SCR_025868 | 2026-08-09 09:08:54 | 1 | |||||||||||
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MySQL-server Resource Report Resource Website 1+ mentions |
MySQL-server (RRID:SCR_025972) | source code, software resource | Open source Relational Database Management System that enables users to store, manage, and retrieve structured data efficiently. | SQL, relational database management system, Structured Query Language Server, | Free, Available for download, Freely available | SCR_025972 | My Structured Query Language Server | 2026-08-09 09:09:21 | 2 | ||||||||||
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STAR-Fusion Resource Report Resource Website 10+ mentions |
STAR-Fusion (RRID:SCR_025853) | source code, software resource | Software tool to leverage chimeric and discordant read alignments identified by STAR aligner to predict fusions. Component of Trinity Cancer Transcriptome Analysis Toolkit. Used to identify candidate fusion transcripts supported by Illumina reads. Maps junction reads and spanning reads to reference annotation set. | identify candidate fusion transcripts, predict fusions, leverages chimeric and discordant read alignments, chimeric, discordant, read alignment, | Howard Hughes Medical Institute ; Klarman Cell Observatory ; NCI U24CA180922; NCI R50CA211461; NCI R21CA209940; NCI U01CA214846 |
PMID:31639029 | Free, Available for download, Freely available | SCR_025853 | 2026-08-09 09:09:20 | 47 | |||||||||
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pracma Resource Report Resource Website 1+ mentions |
pracma (RRID:SCR_026021) | software toolkit, software resource | Software R package provides functions from numerical analysis and linear algebra, numerical optimization, differential equations, time series, plus some well-known special mathematical functions. Uses 'MATLAB' function names where appropriate to simplify porting. | R, numerical analysis functions, linear algebra functions, numerical optimization, differential equations, time series, | Free, Available for download, Freely available | SCR_026021 | Practical Numerical Math Functions, pracma: Practical Numerical Math Functions | 2026-08-09 09:09:22 | 9 | ||||||||||
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MethylSig Resource Report Resource Website 1+ mentions |
MethylSig (RRID:SCR_025849) | software toolkit, software resource | Software R package as whole genome DNA methylation analysis pipeline. Used for testing differentially methylated cytosines or regions in whole-genome bisulfite sequencing or reduced representation bisulfite sequencing experiments. Several options exist for either site-specific or sliding window tests, and variance estimation. | whole genome DNA methylation analysis, whole genome DNA, DNA methylation, testing differentially methylated cytosines, whole-genome bisulfite sequencing, reduced representation bisulfite sequencing, | NCI R01CA158286; NIEHS P30 ES017885 |
PMID:24836530 | Free, Available for download, Freely available | SCR_025849 | 2026-08-09 09:08:53 | 3 | |||||||||
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ZetaStitcher Resource Report Resource Website 10+ mentions |
ZetaStitcher (RRID:SCR_026193) | source code, software resource | Software tool designed to stitch large volumetric images such as those produced by Light-Sheet Fluorescence Microscopes. | Light-Sheet Fluorescence Microscopes, Light-Sheet Fluorescence Microscopes images, stitch large volumetric images, | European Union Horizon 2020 Framework Programme for Research and Innovation | Free, Available for download, Freely available | SCR_026193 | 2026-08-09 09:09:23 | 12 | ||||||||||
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spatial_tri-omics Resource Report Resource Website 1+ mentions |
spatial_tri-omics (RRID:SCR_026194) | source code, software resource | Software repository to share the raw data processing and visualization codes used in the spatial tri-omics project. | raw data processing and visualization codes, spatial tri-omics project, | Free, Available for download, Freely available | SCR_026194 | 2026-08-09 09:08:59 | 2 | |||||||||||
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AutoPVS Resource Report Resource Website |
AutoPVS (RRID:SCR_026108) | software application, software resource | Software automatic classification tool for PVS1 interpretation of null variants. | automatic classification, PVS1 interpretation, null variants, | PMID:32442321 | Free, Available for download, Freely available | https://github.com/JiguangPeng/autopvs1 | SCR_026108 | , Automatic PVS1 interpretation, AutoPVS1 | 2026-08-09 09:09:23 | 0 | ||||||||
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VirtualDub Resource Report Resource Website 10+ mentions |
VirtualDub (RRID:SCR_026123) | software application, software resource | Open-source software for video capture and video processing for Microsoft Windows. Designed to process linear video streams, including filtering and recompression. It uses AVI container format to store captured video. Video capture/processing utility for 32-bit and 64-bit Windows platforms. Used for processing AVI files, although it can read (not write) MPEG-1 and also handle sets of BMP images. | video capture, video processing, process linear video streams, filtering, recompression, processing AVI files, | Free, Available for download, Freely available | https://sourceforge.net/projects/virtualdub/files/ | SCR_026123 | 2026-08-09 09:08:58 | 19 | ||||||||||
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HVSeeker Resource Report Resource Website 1+ mentions |
HVSeeker (RRID:SCR_026120) | software application, software resource | Software tool for distinguishing between bacterial and phage sequences. Consists of two separate models: one analyzing DNA sequences and the other focusing on proteins. | genome, bacteria, phage, sequence, distinguishing between bacterial and phage sequences, | German Research Foundation INST 37/935-1 FUGG; King Fahd University of Petroleum and Minerals |
Free, Available for download, Freely available, | SCR_026120 | 2026-08-09 09:08:58 | 1 | ||||||||||
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Global Environment Facility Resource Report Resource Website |
Global Environment Facility (RRID:SCR_026241) | nonprofit organization, funding resource | Provides information about family of funds for the environment. With GEF support,countries address the root causes of challenges as they strive for international environmental goals. Fund data from the Global Environment Facility. | funds for environment, international environmental goals, | SCR_026241 | 2026-08-09 09:09:24 | 0 | ||||||||||||
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phenoptr Resource Report Resource Website 1+ mentions |
phenoptr (RRID:SCR_026104) | source code, software resource | Software R package for working with inForm data. Contains functions that make it easier to read and analyze data tables and images created by Akoya Biosciences' inForm software. | read data, analyze data, tables and images, Akoya Biosciences, inForm | Free, Available for download, Freely available, | https://github.com/akoyabio/phenoptr | SCR_026104 | 2026-08-09 09:09:23 | 8 | ||||||||||
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WinSCP Resource Report Resource Website 1+ mentions |
WinSCP (RRID:SCR_026226) | software application, software resource | Free file manager, SSH File Transfer Protocol, File Transfer Protocol, WebDAV, Amazon S3, and secure copy protocol client for Microsoft Windows. | file manager, SSH File Transfer Protocol, File Transfer Protocol, WebDAV, Amazon S3, secure copy protocol client, Microsoft Windows, | Free, Available for download, Freely available | SCR_026226 | 2026-08-09 09:09:00 | 5 |
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