Gsea rnk file

If you use gene names, then take note that many gene names are not unique and will need to be collapsed somehow. Jamie 2 March at Mark Ziemann 2 March at Mark Ziemann 17 November at Bridget 17 November at Jagdish chand 28 January at Mark Ziemann 5 October at Lippincott Williams and Wilkins 5 October at Popular posts from this blog Installing R There are some great instructions here but there are a few gotchas to be aware of.

Follow these instructions first, and it will make the process a LOT easier: 1. Make sure you have these dependancies installed. If you don't, you're going to have trouble installing any R packages like R curl, tidyverse, devtools, etc sudo apt install libssl-dev libcurl4-openssl-dev libxml2-dev 2.

Remove any existing R install. Remove any remaining packages. With a single file only the names are necessary. Leave this blank to select all gene sets. If used, a semicolon is recommended. This is true by default, matching the former behavior where a ZIP bundle was always created. Input Files 1. Output Files 1. Task Type: Gene List Selection. This is a file in RNK format that contains the rank ordered gene or feature list. Specifies the number of permutations to perform in assessing the statistical significance of the enrichment score.

Default: The enrichment statistic. After filtering from the gene sets any gene not in the expression dataset, gene sets larger than this are excluded from the analysis. After filtering from the gene sets any gene not in the expression dataset, gene sets smaller than this are excluded from the analysis. Method used to normalize the enrichment scores across analyzed gene sets. Create detailed gene set report heat map, mountain plot, etc.

Default: true. Line format: sample 1 class space sample 2 class space Example: 0 0 Example file : P Continuous phenotypes are used for time series experiments or to find gene sets correlated with a gene of interest gene neighbors.

A CLS file for continuous labels can contain one or more labels. The following example shows a CLS file that defines two continuous labels:. The first line contains the text " numeric" which indicates that the file defines continuous labels.

The remainder of the file defines the continuous phenotypes. For each phenotype:. For a continuous phenotype label, the values for the samples define the phenotype profile. The relative change in the values defines the relative distance between points in the phenotype profile. In the example shown above, the sample values for the two phenotype labels are gene expression values. The phenotype profile is the expression profile for a gene and is used to find gene sets correlated with that gene.

For a time series experiment, you would choose sample values that define the desired expression profile. The example shown below assumes that you have five samples taken at 30 minute intervals.

The first phenotype label defines a phenotype profile that shows steadily increasing gene expression; the second defines a profile that shows an initial peak and then gradual decrease:.

The GMX file format is a tab delimited file format that describes gene sets. The GMX file format is organized as follows:. Each gene set is described by a name, a description, and the genes in the gene set. The GMT file format is a tab delimited file format that describes gene sets.

The GMT file format is organized as follows:. The GRP files contain a single gene set in a simple newline-delimited text format. The GRP file format is organized as follows:. The MDB files contain an entire gene set database. The CHIP file contains annotation about a microarray.

It should list the features i. All gene sets only Gene Ontology. Caenorhabditis elegans nematode. Canis familiaris dog. Danio rerio zebrafish. Drosophila melanogaster fruit-fly. Equus ferus caballus horse. Felis catus cat. Gallus gallus chicken. Homo sapiens human. Oryctolagus cuniculus rabbit. Pan troglodytes chimpanzee. Rattus norvegicus brown rat. Sus scrofa pig. Xenopus tropicalis frog. Dictyostelium discoideum slime mold. Leishmania major aleppo boil. Plasmodium falciparum malarial parasite.

Escherichia coli k12 intestinal bacteria. Brachypodium distachyon purple false brome. Glycine max soybean. Hordeum vulgare barley. Oryza sativa Asian rice.