User: lm795

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lm7950
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Posts by lm795

<prev • 10 results • page 1 of 1 • next >
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Problems with creating phyloseq bar plots from a table with species data
... I am trying to plot species abundance for intestinal bacteria analysed using a 16S RNA sequencing method. I am using RStudio (1.1.456) and R 3.5.1 My input is a file called "Species_percentages_test.csv", [here][1]. I was following the tutorial on "[Importing phyloseq Data][2]", more specifically, l ...
phyloseq microbiome analysis written 5 weeks ago by lm7950
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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 ...
microarray bioconductor mapfromtranscripts cytoscape written 5 months ago by lm7950
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Comment: C: Getting R to talk to BioMart using biomaRt
... Many thanks Mike, the issue is now resolved. ...
written 5 months 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 5 months 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 5 months 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 5 months 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 5 months 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 5 months 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 5 months 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 5 months ago by lm7950 • updated 5 months ago by James W. MacDonald49k

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