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https://github.com/virajbdeshpande/AmpliconArchitect

Software package designed to call circular DNA from short read WGS data.Used to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates architecture of amplicon.Used to reconstruct structure of focally amplified regions using whole genome sequencing and validate it extensively on multiple simulated and real datasets, across wide range of coverage and copy numbers.

Proper citation: AmpliconArchitect (RRID:SCR_023150) Copy   

•   Source: SciCrunch Registry

https://github.com/findCP/findCPcli

Software command line Python package for computation of chokepoint reactions in genome scale metabolic models. Used to compute chokepoints by taking into account both topology and dynamic information of network. Can compute and remove dead-end metabolites, find essential reactions and update flux bounds of reactions according to results of Flux Variability Analysis.

Proper citation: findCPcli (RRID:SCR_023391) Copy   

•   Source: SciCrunch Registry

https://github.com/lufuhao/mitochondria-simulator

Software repository for mtDNA assembly project.

Proper citation: mitochondria simulator (RRID:SCR_023430) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/synchCams/

Software toolbox for synchronized dual camera acquisition. Library for acquisition of synchronized dual camera video. Videos are saved with alternate acquisition of frames what ensures equal number of frames.

Proper citation: synchCams (RRID:SCR_023152) Copy   

•   Source: SciCrunch Registry

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

Software R package as set of standards that specify common storage and access model of geographic features made of mostly two dimensional geometries used by geographic information systems. Standardized way to encode spatial vector data. Formalized by Open Geospatial Consortium and International Organization for Standardization.

Proper citation: Simple Features (RRID:SCR_023393) Copy   

•   Source: SciCrunch Registry

http://szhorvat.net/pelican/igraphm-a-mathematica-interface-for-igraph.html

Software package for use in complex networks and graph theory research. Mathematica interface for igraph. Provides Mathematica interface to popular igraph network analysis package, as well as many other functions for working with graphs in Mathematica. IGraph/M comes pre-packaged and ready to use on Windows, OS X and Linux (64-bit Intel), as well as the Raspberry Pi computer. The code is open source and can be compiled on other platforms as well (such as 32-bit Windows).

Proper citation: iGraph/M (RRID:SCR_023308) Copy   

•   Source: SciCrunch Registry

https://github.com/qianli10000/mtradeR

Software R package implements Joint model with Matching and Regularization and simulation pipeline. Used to test association between taxa and disease risk, and adjusted for correlated taxa screened by pre-selection procedure in abundance and prevalence, individually.

Proper citation: mtradeR (RRID:SCR_022977) Copy   

•   Source: SciCrunch Registry

https://github.com/compbiolabucf/omicsGAN

Software generative adversarial network to integrate two omics data and their interaction network to generate one synthetic data corresponding to each omics profile that can result in better phenotype prediction. Used to capture information from interaction network as well as two omics datasets and fuse them to generate synthetic data with better predictive signals.

Proper citation: OmicsGAN (RRID:SCR_022976) Copy   

•   Source: SciCrunch Registry

https://github.com/mgharvey/misc_python/blob/master/bin/TreeMix/treemix_tree_with_bootstraps.py

Phython script for bootstraping Treemix snp trees to generate confidance intervals in the main tree.

Proper citation: treemix_tree_with_bootstraps.py (RRID:SCR_023426) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/org.Mm.eg.db/

Software package for genome wide annotation for mouse, primarily based on mapping using Entrez Gene identifiers.

Proper citation: org.Mm.eg.db (RRID:SCR_023488) Copy   

•   Source: SciCrunch Registry

https://github.com/Shenhav-and-Korem-labs/SCRuB

Software R package to help researchers address common issue of contamination in microbial studies. Well aware MiSeq decontamination program.

Proper citation: SCRuB (RRID:SCR_023518) Copy   

•   Source: SciCrunch Registry

https://www.vosviewer.com/

Software tool for constructing and visualizing bibliometric networks. These networks may for instance include journals, researchers, or individual publications, and they can be constructed based on citation, bibliographic coupling, co-citation, or co-authorship relations. Offers text mining functionality that can be used to construct and visualize co-occurrence networks of important terms extracted from body of scientific literature.

Proper citation: VOSviewer (RRID:SCR_023516) Copy   

•   Source: SciCrunch Registry

https://github.com/genome/bam-readcount

Software tool that runs on BAM or CRAM file and generates low level information about sequencing data at specific nucleotide positions. Its outputs include observed bases, readcounts, summarized mapping and base qualities, strandedness information, mismatch counts, and position within the reads.

Proper citation: bam readcount (RRID:SCR_023653) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=BoutrosLab.plotting.general

Software R package contains several plotting functions such as barplots, scatterplots, heatmaps, as well as functions to combine plots and assist in creation of these plots. Functions to create publication quality plots.

Proper citation: BPG (RRID:SCR_023652) Copy   

•   Source: SciCrunch Registry

https://www.transnetyx.com/colony?gad=1&gclid=CjwKCAjw8symBhAqEiwAaTA__GhOxQovqufxibmOSyRqtSo__-EMrnF9OGpdOAvAPgUOTE47h8TONBoCyMMQAvD_BwE

Software for mouse colony management. Streamlined software for simplified colony management.

Proper citation: Transnetyx Colony Management (RRID:SCR_023922) Copy   

•   Source: SciCrunch Registry

http://statbio.github.io/Sargasso/

Software Python tool to disambiguate mixed species RNA-seq reads according to their species of origin.

Proper citation: Sargasso (RRID:SCR_023489) Copy   

•   Source: SciCrunch Registry

http://samtools.github.io/htsjdk/

Software implementation of unified Java library for accessing common file formats, such as SAM and VCF, used for high-throughput sequencing data. There are also an number of useful utilities for manipulating HTS data.

Proper citation: HTSJDK (RRID:SCR_024036) Copy   

•   Source: SciCrunch Registry

http://proteomics.ucsd.edu/Software/Inspect/

Software tool to addresses several algorithmic problems in order to identify modified proteins.Software MS/MS database search tool specifically designed to address two crucial needs of the proteomics comminuty: post-translational modification identification and search speed.

Proper citation: InsPecT (RRID:SCR_024038) Copy   

•   Source: SciCrunch Registry

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

Software package implements Bayesian multilevel models in R using probabilistic programming language Stan.

Proper citation: brms (RRID:SCR_023862) Copy   

•   Source: SciCrunch Registry

https://github.com/brainglobe/brainreg

Software Python based tool that registers the template brain (e.g. from the Allen Reference Atlas) to the sample image.Automated 3D brain registration with support for multiple species and atlases.

Proper citation: Brainreg (RRID:SCR_023858) Copy   

•   Source: SciCrunch Registry