How to perform KEGG and GO enrichment analysis of non-model species (using R)

This post describes in detail how to perform KO and GO enrichment analyses of a non-model species whose genes/proteins have been annotated using the eggNOG-mapper. This post is mainly so I don't forget the procedures but I hope it can be helpful to others who, like me, just started out doing omics analyses on non-model …

AndreiColors: R color palette package, inspired by the movies of Andrei Arsenyevich Tarkovsky

https://github.com/JoshEbner/AndreiColors I wrote a little R package using still frames of the movies by Andrei Tarkovsky (Андрей Арсеньевич Тарковский). He was a Soviet and Russian filmmaker and film theorist. He is widely considered one of the greatest and most influental directors in the history of Russian and world cinema. Follow the github link for more …

Construct a custom protein database of a non-model species

This post describes a very simply pipeline on how to create a protein database file from predicted genes (from de novo transcriptome assemblies using Trinity) that can be imported into proteomics software such as MaxQuant, MSFragger and co. as a database. This facilitates the identification of (sometimes novel) proteins from mass spectrometry derived spectral data …

Geschützt: Principal coordinates of neighbour matrices (PCNM) aka. Moran’s Eigenvector Maps (MEM) in R (Unfinished)

Es gibt keine Kurzfassung, da dies ein geschützter Beitrag ist.

RQL/RLQ Analysis (concept and R implementation)

RLQ analysis is a method by which one might uncover how "the environment" filters certain species traits. For example, one can determine whether a particular environment (defined by a site x environment table; the environment is "whatever one wants it to be: e.g. abiotic (temperature, conductivity, wind-speed, UV-radiation, soil-type etc.)) selects for species with e.g. …

Fuzzy Set Ordination (FSO) in R

This post aims at laying out the reasoning, methodology and implications of Fuzzy Set Ordination (FSO), a statistical technique on which I could neither find a blog post nor a pdf file on the internet that would aim at explaining this method for the under- or post-graduate busying him- or herself with the study of …

Distance-based redundancy analysis (db-RDA) in R

Distance-based redundancy analysis (db-RDA) is a method for carrying out constrained ordinations on data using non-Euclidean distance measures. A distance matrix is calculated using the distance measure of choice A principle coordinates analysis (PCoA) is done on the matrix The eigenvectors obtained in the PCoA are plugged into an RDA This statistical method is a …

Permutational Multivariate Analysis of Variance (PERMANOVA) in R

In many biological, ecological, and environmental data sets, the assumptions of MANOVA (MANOVA (Multivariate analysis of variance) in R (short)) are not likely to be met. A number of more robust methods to compare groups of multivariate sample units have been proposed and several of these have now become very widely used in ecology. They …

MANOVA (Multivariate analysis of variance) in R (short)

Multivariate analysis of variance (MANOVA) is a procedure for comparing multivariate sample means. As a multivariate procedure, it is used when there are two or more dependent variables, and is typically followed by significance tests involving individual dependent variables seperately. It helps to answer: Do changes in the independent variable(s) have significant effects on the …

Biodiversity. Indices, concepts and R implementations (in progress).

Callicott et al. (1999) examined "biodiversity" as one of the current normative concepts in conservation. They concluded that it remains ill-defined, and that distinctions can be made between "functional" and "compositional" perspectives in approaching biodiversity. “Functional” refers to a primarily concern with ecosystem and evolutionary processes, while “compositional” sees organisms as aggregated into populations, species, higher …