Tools   Select Another Resource Report Type

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://metacpan.org/dist/Bio-Chado-Schema

Standard object-relational mapping layer for use with GMOD Chado database schema. This layer is implemented with DBIx::Class, generated with the help of DBIx::Class::Schema::Loader module.

Proper citation: Bio-Chado-Schema (RRID:SCR_024059) 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

https://github.com/wkusmirek/mONiTor

Software tool monitors metrics available in sequencer, state of the computer to which the sequencer is connected, and the contents of the fast5 and fastq files. Real-time monitoring of Oxford Nanopore Technology sequencing run. Used for monitoring nanopore sequencing process.

Proper citation: mONiTor (RRID:SCR_023921) 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

https://ginkgo-cadx.com/en/

Software advanced DICOM viewer and dicomizer that can also be used to convert png, jpeg, bmp, pdf, tiff to DICOM files.

Proper citation: Ginkgo CADx (RRID:SCR_024031) 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

https://github.com/PolarBean/DeepSlice?

Software Python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning.

Proper citation: DeepSlice (RRID:SCR_023854) Copy   

•   Source: SciCrunch Registry

http://bibus-biblio.sourceforge.net/

Bibliographic and reference management software. Allows to search, edit, and sort bibliographic records.

Proper citation: Bibus (RRID:SCR_023974) Copy   

•   Source: SciCrunch Registry

http://mouse.brainarchitecture.org/cell-type-analysis-toolbox

Software toolbox is cell counting and distribution mapping platform which can be used to analyze serial two-photon tomography (STPT) data.

Proper citation: Cell Type Analysis Toolbox (RRID:SCR_023852) Copy   

•   Source: SciCrunch Registry

https://github.com/klebgenomics/Kaptive

Software tool to report information about surface polysaccharide loci for Klebsiella pneumoniae species complex and Acinetobacter baumannii genome assemblies.

Proper citation: Kaptive (RRID:SCR_024046) Copy   

•   Source: SciCrunch Registry

https://www.jabref.org/

Open source, software cross platform citation and reference management tool.Helps to collect and organize sources, find the paper, discover the latest research.

Proper citation: JabRef (RRID:SCR_024047) Copy   

•   Source: SciCrunch Registry