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DESeq is a Bioconductor package to perform differential gene expression analysis based on negative binomial distribution. DEGSeq; Derfinder Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach. DEvis is a powerful, integrated solution for the analysis of differential expression ...
Name Description Knots [Note 1]Links References trRosettaRNA: trRosettaRNA is an algorithm for automated prediction of RNA 3D structure. It builds the RNA structure by Rosetta energy minimization, with deep learning restraints from a transformer network (RNAformer). trRosettaRNA has been validated in blind tests, including CASP15 and RNA-Puzzles, which suggests that the automated predictions ...
Anduril is an open source component-based workflow framework for scientific data analysis [2] developed at the Systems Biology Laboratory, University of Helsinki.. Anduril is designed to enable systematic, flexible and efficient data analysis, particularly in the field of high-throughput experiments in biomedical research.
The Simple Function Point (SFP) method [1] is a lightweight Functional Measurement Method. The Simple Function Point method was designed by Roberto Meli in 2010 to be compliant with the ISO14143-1 standard and compatible with the International Function Points User Group (IFPUG) Function Point Analysis (FPA) method.
Gene set enrichment determines if the overlap between two gene sets is statistically significant, in this case the overlap between differentially expressed genes and gene sets from known pathways/databases (e.g., Gene Ontology, KEGG, Human Phenotype Ontology) or from complementary analyses in the same data (like co-expression networks).
In bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution. It can be performed on the entire genome, transcriptome or proteome of an organism, and can also involve only selected segments or regions ...
The process of gene expression is used by all known life—eukaryotes (including multicellular organisms), prokaryotes (bacteria and archaea), and utilized by viruses—to generate the macromolecular machinery for life. In genetics, gene expression is the most fundamental level at which the genotype gives rise to the phenotype, i.e. observable ...
In the field of molecular biology, gene expression profiling is the measurement of the activity (the expression) of thousands of genes at once, to create a global picture of cellular function. These profiles can, for example, distinguish between cells that are actively dividing, or show how the cells react to a particular treatment.