What are RIKEN genes? - Bioinformatics Stack Exchange
There are some specific genes with name ending with suffix 'Rik' (e.g. 0610005C13Rik or 0610007C21Rik). Searching online I found that they are from RIKEN project.
Prune GTDB phylogenetic trees to given taxonomic resolution
Aug 6, 2025 · I need some help in modifying GTDB's phylogenetic trees to achieve a given taxonomic resolution. I have downloaded the Archaea and Bacteria trees from GTDB's repo …
Common gene naming conventions and how to convert between them
Mar 19, 2021 · These look like Mouse Gene identifiiers. You might be able to use org.Mm.eg.db to map them to aliases. There should be a way to use biomaRt as well, but I don't know the speciifics - …
chip seq - Nextflow error: “Invalid method invocation call with ...
Nov 3, 2025 · I’m building a ChIP-Seq pipeline in Nextflow, and I’m running into this persistent error when trying to connect two processes that utilize HOMER's ...
python - How to perform liftover from 38 to 37 in R? - Bioinformatics ...
Nov 18, 2023 · I have some gwas summary statistics in GRCh38 that I want to lift to GRCh37. I am trying to liftover in R using this code: library (tidyverse) library (magrittr) library (data.table) library …
r - How to find closely related genes for a specific gene from WGCNA ...
Oct 29, 2022 · The simplest way is to re-calculate (or load, if saved) the TOM matrix and find the genes with the highest TOM to MALAT1. If you have enough RAM to carry out WGCNA in a single block, …
Increase number of threads for GATK 4.0 HaplotypeCaller
I am assuming you are using the non-SPARK version of the method. To specify the number of threads you wish to use with HaplotypeCaller, include --native-pair-hmm-threads (). This will only parallelize …
how is log2foldchange calculated in DESeq2
Sep 22, 2023 · I am trying to calculate log2FoldChange in DESeq2 by hand because I am trying to reproduce my results and understand how DESeq2 works. What I want to know is: Are the counts …
r - How to correct alpha, and not p-values themselves, for ...
Jun 13, 2017 · I have a set of differentially methylated/expressed/whatever entities with p-values attached (example below). entity_name p-value magnitude entity1 0.04459 0.68 entity2 0.02...
How to compare CDS, CNE, miRNA, UCNE across new related genomes?
Apr 12, 2024 · How do the reference genomes map onto the raw data you have? E.g. you have a big species complex or genus with several species, and there are 8 species, of which 3 have reference …