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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.
PathwaySeq [154] Pathway analysis for RNA-Seq data using a score-based approach. petal Co-expression network modelling in R. ToPASeq: [155] an R package for topology-based pathway analysis of microarray and RNA-Seq data. RNA-Enrich A cut-off free functional enrichment testing method for RNA-seq with improved detection power.
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Visualize next generation sequencing data (BAM files) using UGENE Assembly Browser; Variant calling with SAMtools [8] RNA-Seq data analysis with Tuxedo pipeline (TopHat, [9] Cufflinks, [10] etc.) ChIP-seq data analysis with Cistrome pipeline (MACS, [11] CEAS, [12] etc.) Raw NGS data processing; HMMER 2 and 3 packages integration; Chromatogram ...
It is the first step in sequence analysis to limit wrong conclusions due to poor quality data. The tools used at this stage depend on the sequencing platform. For instance, FastQC checks the quality of short reads (including RNA sequences), Nanoplot or PycoQC are used for long read sequences (e.g. Nanopore sequence reads), and MultiQC ...
Wilbanks and colleagues [3] is a survey of the ChIP-seq peak callers, and Bailey et al. [4] is a description of practical guidelines for peak calling in ChIP-seq data. Peak calling may be conducted on transcriptome/exome as well to RNA epigenome sequencing data from MeRIPseq [ 5 ] or m6Aseq [ 6 ] for detection of post-transcriptional RNA ...
Illumina sequencing: it offers a good method for small RNA sequencing and it is the most widely used approach. [7] After the library preparation and amplification steps, the sequencing (based on the use of reversible dye-terminators ) can be performed by using different systems, such as Miseq System, Miseq Series, NextSeq Series and many others ...
The RNA-SSD (RNA Secondary Structure Designer) approach first assigns bases probabilistically to each position based probabilistic models. Subsequently, a stochastic local search is used to optimize this sequence. RNA-SSD is publicly available under the name of RNA Designer at the RNASoft web page: Web Server [197] INFO-RNA