User: lm795

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lm7950
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United Kingdom
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1 month, 2 weeks ago
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2 months, 1 week ago
Email:
l****@mrc-tox.cam.ac.uk
I am a programme leader at the MRC Toxicology Unit. The aim of my research programme is understanding the cellular and molecular mechanisms that mitochondria use, as signaling hubs, for coping with toxic insults.

Posts by lm795

<prev • 9 results • page 1 of 1 • next >
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Exploring upstream regulators (transcription factors, drugs, etc) of transcripts in R
... I am interesting in identifying upstream regulators of a filtered group of transcripts, identified using either microarray or RNAseq technology. In the past, I have used Ingenuity Pathway Analysis (IPA) from QIAGEN. IPA's Comparison Analysis uses an Upstream Regulator analytic sub-routine. This pro ...
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Comment: C: Getting R to talk to BioMart using biomaRt
... Many thanks Mike, the issue is now resolved. ...
written 8 weeks ago by lm7950
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Comment: C: Getting R to talk to BioMart using biomaRt
... Ok, I have Dropboxed gene_ids, with the header as a csv file here. Thanks again! ...
written 9 weeks ago by lm7950
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Comment: C: Getting R to talk to BioMart using biomaRt
...   Hi again, I have troubleshooted and got it to work with Mike's example. Here is my code: # Project 01: Annotate Drosophila gene IDs with human IDs from BioMart # Loading the required libraries library(tidyverse) library(biomaRt) gene_list <- read_csv("/Users/miguel/Dropbox/RStudio/Martins_ ...
written 9 weeks ago by lm7950
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Comment: C: Getting R to talk to BioMart using biomaRt
... Thanks James, I will troubleshoot my code and when I do so post an update here. I am unfamiliar on how to post properly formatted code in this platform, is there a tutorial available? ...
written 9 weeks ago by lm7950
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Comment: C: Getting R to talk to BioMart using biomaRt
... Thanks James, I have tried getBM but will dive into getLDS soon. As you see from above I am still having a few issues with getBM ...
written 9 weeks ago by lm7950
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Comment: C: Getting R to talk to BioMart using biomaRt
...   Hi again, I used the getBM function using the following code: library(tidyverse) library(dplyr) gene_list <- read_csv("/Users/miguel/Dropbox/RStudio/Martins_Sanz/data/Thermal_Stress_GSA.csv") gene_ids <- gene_list %>%   select (Gene_ID) # ****Note that there is a bug and if biomaRt is ...
written 9 weeks ago by lm7950
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Comment: C: Getting R to talk to BioMart using biomaRt
... Many thanks for the very useful explanation Mike, I will give it a go with my table. I will come back if I encounter problems. I am a bit of a rookie ...
written 9 weeks ago by lm7950
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Getting R to talk to BioMart using biomaRt
... Greetings! I am new to this forum and posted a question recently to the RStudio community. A kind soul, Mara Averick pointed me to this forum. My objective is to annotate a table of gene expression data "say for organism A" with information on orthologues from "organism B", as an additional column ...
biomart written 9 weeks ago by lm7950 • updated 9 weeks ago by James W. MacDonald48k

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