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DESeq2 is a software package in the field of bioinformatics and computational biology for the statistical programming language R. It is primarily employed for the analysis of high-throughput RNA sequencing (RNA-seq) data to identify differentially expressed genes between different experimental conditions.
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Within computational biology, an MA plot is an application of a Bland–Altman plot for visual representation of genomic data. The plot visualizes the differences between measurements taken in two samples, by transforming the data onto M (log ratio) and A (mean average) scales, then plotting these values.
pyOpenMS is an open-source Python library for mass spectrometry, specifically for the analysis of proteomics and metabolomics data in Python. Peaksel Proprietary: This web-based (available both in cloud as SaaS and as on-prem installation) software for LC/MS data processing supports batch processing and high-throughput experiments.
Packages like ggplot2 in R and Matplotlib in Python are often used to create the visuals. The table can also be annotated using a reference annotation file, usually in GTF or GFF format to provide more context about the genes, such as the chromosome name, strand, and start and positions, and aid result interpretation.
A Canonical XML document is by definition an XML document that is in XML Canonical form, defined by The Canonical XML specification. Briefly, canonicalization removes whitespace within tags, uses particular character encodings, sorts namespace references and eliminates redundant ones, removes XML and DOCTYPE declarations, and transforms ...
Sphinx converts reStructuredText files into HTML websites and other formats including PDF, EPub, Texinfo and man.. reStructuredText is extensible, and Sphinx exploits its extensible nature through a number of extensions – for autogenerating documentation from source code, writing mathematical notation or highlighting source code, etc.
reStructuredText (RST, ReST, or reST) is a file format for textual data used primarily in the Python programming language community for technical documentation.. It is part of the Docutils project of the Python Doc-SIG (Documentation Special Interest Group), aimed at creating a set of tools for Python similar to Javadoc for Java or Plain Old Documentation (POD) for Perl.