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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.
fastqp Simple FASTQ quality assessment using Python. Kraken: [9] A set of tools for quality control and analysis of high-throughput sequence data. HTSeq [10] The Python script htseq-qa takes a file with sequencing reads (either raw or aligned reads) and produces a PDF file with useful plots to assess the technical quality of a run.
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The BED (Browser Extensible Data) format is a text file format used to store genomic regions as coordinates and associated annotations. The data are presented in the form of columns separated by spaces or tabs. This format was developed during the Human Genome Project [1] and then adopted by other sequencing
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.
In morphology and lexicography, a lemma is the canonical form of a set of words. In English, for example, run, runs, ran, and running are forms of the same lexeme, so we can select one of them; ex. run, to represent all the forms. Lexical databases such as Unitex use this kind of representation.
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.
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