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

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.

Proper citation: MSM (RRID:SCR_015500) Copy   

•   Source: SciCrunch Registry

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

Software R package for phylogenetic comparative biology. The package contains various functions for phylogenetic analysis of comparative data from species.

Proper citation: phytools (RRID:SCR_015502) Copy   

•   Source: SciCrunch Registry

https://github.com/lucventurini/mikado/

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.

Proper citation: Mikado (RRID:SCR_016159) Copy   

•   Source: SciCrunch Registry

http://github.com/fraimondo/cudaica

Software that implements Infomax ICA, which is an algorithm to perform Independent Component Analysis, in CUDA (a parallel computing platform and programming model).

Proper citation: CUDAICA (RRID:SCR_015630) Copy   

•   Source: SciCrunch Registry

https://cell-innovation.nig.ac.jp/maser/Tools/visualization_top_en.html

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).

Proper citation: regist custom genome (RRID:SCR_015999) Copy   

•   Source: SciCrunch Registry

https://github.com/Neuroinflab/kCSD-python

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.

Proper citation: kCSD-python (RRID:SCR_015777) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/lme4/index.html

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."

Proper citation: lme4 (RRID:SCR_015654) Copy   

•   Source: SciCrunch Registry

https://pythonvideoannotator.readthedocs.io/en/master/index.html

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.

Proper citation: PythonVideoAnnotator (RRID:SCR_025868) Copy   

•   Source: SciCrunch Registry

https://github.com/mysql/mysql-server

Open source Relational Database Management System that enables users to store, manage, and retrieve structured data efficiently.

Proper citation: MySQL-server (RRID:SCR_025972) Copy   

•   Source: SciCrunch Registry

https://github.com/STAR-Fusion/STAR-Fusion

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.

Proper citation: STAR-Fusion (RRID:SCR_025853) Copy   

•   Source: SciCrunch Registry

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

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.

Proper citation: pracma (RRID:SCR_026021) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/bioc/html/methylSig.html

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.

Proper citation: MethylSig (RRID:SCR_025849) Copy   

•   Source: SciCrunch Registry

https://github.com/lens-biophotonics/ZetaStitcher

Software tool designed to stitch large volumetric images such as those produced by Light-Sheet Fluorescence Microscopes.

Proper citation: ZetaStitcher (RRID:SCR_026193) Copy   

•   Source: SciCrunch Registry

https://github.com/di-0579/spatial_tri-omics

Software repository to share the raw data processing and visualization codes used in the spatial tri-omics project.

Proper citation: spatial_tri-omics (RRID:SCR_026194) Copy   

•   Source: SciCrunch Registry

https://autopvs1.bgi.com/

Software automatic classification tool for PVS1 interpretation of null variants.

Proper citation: AutoPVS (RRID:SCR_026108) Copy   

•   Source: SciCrunch Registry

https://www.virtualdub.org

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.

Proper citation: VirtualDub (RRID:SCR_026123) Copy   

•   Source: SciCrunch Registry

https://github.com/BackofenLab/HVSeeker/tree/main

Software tool for distinguishing between bacterial and phage sequences. Consists of two separate models: one analyzing DNA sequences and the other focusing on proteins.

Proper citation: HVSeeker (RRID:SCR_026120) Copy   

•   Source: SciCrunch Registry

https://www.thegef.org/projects-operations/recipient-countries/

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.

Proper citation: Global Environment Facility (RRID:SCR_026241) Copy   

•   Source: SciCrunch Registry

https://akoyabio.github.io/phenoptr/index.html

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.

Proper citation: phenoptr (RRID:SCR_026104) Copy   

•   Source: SciCrunch Registry

https://winscp.net/eng/download.php

Free file manager, SSH File Transfer Protocol, File Transfer Protocol, WebDAV, Amazon S3, and secure copy protocol client for Microsoft Windows.

Proper citation: WinSCP (RRID:SCR_026226) Copy   

•   Source: SciCrunch Registry