Our January newsletter includes thirteen new and updated software titles and fifty four new R packages available in R 3.6.2. This new release of R is also available for use with Jupyter notebooks. Spring training schedules include sixteen workshops and classes available to HMS researchers.
We remind readers that BioGrids is not compatible with MacOS 10.15 at this time.
While we recommend not upgrading to 10.15 on any Mac with BioGrids already installed, we have implemented a workaround to install BioGrids and SBGrid on new machines.
If your use of BioGrids supplied software was an important element in your publication, please include the following statement in your work:
"Software used in the project was installed and configured by BioGrids
(cite: eLife 2013;2:e01456, Collaboration gets the most out of software.)"
Register here to try out our software installer, which allows users to choose from over 290 bioinfomatics and life sciences tools that can be installed as ready-to-run applications on Mac or Linux machines with the click of a button or a short command from the CLI. No need to worry about dependencies or compilation.
BioGrids is supported by a team of scientists and engineers at HMS. We provide direct support to BioGrids members. This includes all aspects of software installation and management. If you need assistance of any kind please send a note to: firstname.lastname@example.org.
The BioGrids Installer is an easy to use application that makes installing and managing life sciences software simple and quick.
A command line version is also available for Macs and Linux. Download using the link button above and register here for activation.
The BioGrids team provides support, infrastructure and testing for scientific software packages. We currently provide over 290 titles in five categories and an additional 1,500 R, python and perl packages and modules. The collection grows weekly. Learn more here: About BioGrids
If you are new to BioGrids and would like to quickly get started with the command line version, follow the instructions below:
1: Download the BioGrids Installer command line version
./biogrids activate biogrid-production jvinent1 70rYFTDnmCr93VUklfbf1s3M4jdyC9bFVYHew==
Replace the site name, user name and activation key with your own credentials.
3: Install software with BioGrids
./biogrids install fastqc trimmomatic samtools star subread igv
When finished, verify applications are installed:
Anvi'o is an open-source, community-driven analysis and visualization platform for ‘omics data. It brings together many aspects of today’s cutting-edge genomic, metagenomic, metatranscriptomic, pangenomic, and phylogenomic analysis practices to address a wide array of needs.
BLAST+ is a suite of BLAST (Basic Local Alignment Search Tool) tools that utilizes the NCBI C++ Toolkit with a number of performance and feature improvements over the legacy BLAST applications.
gffread validates, filters, converts and performs various other operations on GFF files (use gffread -h to see the various usage options).
GFOLD computes a generalized fold change for ranking differentially expressed genes from RNA-seq data.
IGV (Integrative Genomics Viewer) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
MAGeCK Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens (or GeCKO) technology.
MAGeCK-VISPR is a comprehensive quality control, analysis and visualization workflow for CRISPR/Cas9 screens.
Mono is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime.
MRtrix3 provides a set of tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses.
R is a free software environment for statistical computing and graphics. BioGrids R includes 434 packages.
PyCharm is a dedicated Python Integrated Development Environment (IDE) providing a wide range of essential tools for Python developers, tightly integrated together to create a convenient environment for productive Python, web, and data science development.
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.
TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.