Software Updates

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

a comprehensive quality control, analysis and visualization workflow for CRISPR/Cas9 screens.

GFOLD

GFOLD stands for Generalized FOLD change for ranking differentially expressed genes from RNA-seq data. GFOLD is especially useful when no replicate is available. GFOLD generalizes the fold change by considering the posterior distribution of log fold change, such that each gene is assigned a reliable fold change. It overcomes the shortcoming of p-value that measures the significance of whether a gene is differentially expressed under different conditions instead of measuring relative expression changes, which are more interesting in many studies. It also overcomes the shortcoming of fold change that suffers from the fact that the fold change of genes with low read count are not so reliable as that of genes with high read count, even these two genes show the same fold change.

R

a free software environment for statistical computing and graphics.

MRtrix3

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.

Anvi'o

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.

MRtrix3

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.

TransDecoder

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.

PyCharm

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

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. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments longer sequences that have been assembled from those reads. In order to identify differentially expressed genes between experiments, StringTie's output can be processed by specialized software like Ballgown, Cuffdiff or other programs (DESeq2, edgeR, etc.).

gffread

validates, filters, converts and performs various other operations on GFF files (use gffread -h to see the various usage options). Because the program shares the same GFF parser code with Cufflinks, Stringtie, and gffcompare, it could be used to verify that a GFF file from a certain annotation source is correctly "understood" by these programs. Thus the gffread utility can be used to simply read the transcripts from the file, and optionally print these transcripts back, in either GFF3 (default) or GTF2 format (with the -T option), while discarding any non-essential attributes, optionally fixing some potential issues with the input file(s).

BLAST+

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.

IGV

(Integrative Genomics Viewer) 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.