User: c.e.chong

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c.e.chong20
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Posts by c.e.chong

<prev • 44 results • page 1 of 5 • next >
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(Closed) Deseq2 : Error some values in assay are not integers
... Hi all, I'm trying to construct deseq2 dataset object using : countData <- read.csv('ddtry2000.csv',sep = ",", header = TRUE, row.names = 1) metaData <- read.table('metadatakegg.txt', header = TRUE, sep = "\t", row.names = 1) #construct deseq dataset object keggdds &l ...
R metagenomics rna-seq written 9 weeks ago by c.e.chong20
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Comment: C: Import metaphlan output to phyloseq
... Hi dpc, These were my R commands : ########## library(phyloseq) library(DESeq2) library(ggplot2) library(curatedMetagenomicData) mphlanin <- read.csv("merged_abundance_table_reformatted.txt", sep = "\t", strip.white = T, stringsAsFactors = F, row.names = 1) metadata ...
written 9 weeks ago by c.e.chong20
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Comment: C: Import metaphlan output to phyloseq
... Hi, I've seen a a few of your posts @dpc and it seems like we're trying to do the same thing. I have used metphlantophyloseq.r functions to get my metaphlan rel ab data into phyloseq and want to put this into Deseq2. Did you manage to do this? Did you covert the relative abundance into raw counts ...
written 10 weeks ago by c.e.chong20
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Comment: C: Importing MetaPhlAn3 profile table into phyloseq to use decontam
... Thank you so much for your help. I have managed to recreate what you did with this function. The function on wipperman GitHub however does not create a sample_data() as well as the tax table and out table which I need. The function from the Waldron lab that you linked first on this post does, but I ...
written 10 weeks ago by c.e.chong20
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Comment: C: What are the input files for lwaldron / metaphlanToPhyloseq.R ?
... Thank you so much for your help! I'm still getting an error. I have a directory called metaphlan_profiling and it contains 22 .txt outputs from metaphlan mtph_subDir <- "metaphlan_profiling/" I read in the metadata information (I'm not sure if this should be a data frame) metadat ...
written 10 weeks ago by c.e.chong20
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Comment: C: What are the input files for lwaldron / metaphlanToPhyloseq.R ?
... Ok, so I should run through the ‘curatedMetagenomicData’ pipeline with my data? ...
written 10 weeks ago by c.e.chong20
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Comment: C: What are the input files for lwaldron / metaphlanToPhyloseq.R ?
... Thank you for getting back to me. I've tried this and get this error: metaphlan <- read.csv("statemerged_abundance_table_reformatted.csv", header = TRUE) metadata <- read.delim("metadata.txt", header = FALSE, sep = "\t") metaphlanToPhyloseq(metaphlandir = metaphlan, metadat = me ...
written 10 weeks ago by c.e.chong20
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What are the input files for lwaldron / metaphlanToPhyloseq.R ?
... Hi, Has anyone used lwaldron/metaphlanToPhyloseq.R (https://gist.github.com/lwaldron/512d1925a8102e921f05c5b25de7ec94)? I'm unsure of what the input files should be and there is no help information on GitHub. I'm wanting to use it to input my metaphlan3 merged abundance table into phyloseq. Th ...
R metagenomics metaphlan written 10 weeks ago by c.e.chong20 • updated 10 weeks ago by zorbax210
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Comment: C: Importing MetaPhlAn3 profile table into phyloseq to use decontam
... I have run metaphlan3 and have a merged abundance output file that looks like this : clade_name healthy_mphlan dandruff_mphlan dandruffhealthy_mphlan k__Bacteria 91.40268 71.86512 89.7509 k__Bacteria|p__Actinobacteria 86.36566 49.51296 77.30806 k__Bacteria|p__Actinobacteria|c__Actin ...
written 10 weeks ago by c.e.chong20
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Comment: C: Importing MetaPhlAn3 profile table into phyloseq to use decontam
... Hi, did you manage to figure this out? I'm trying to do the same thing and I'm getting this error! ...
written 10 weeks ago by c.e.chong20

Latest awards to c.e.chong

Popular Question 8 weeks ago, created a question with more than 1,000 views. For Kraken2 to Phyloseq
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Popular Question 15 months ago, created a question with more than 1,000 views. For bbmap split paired-end reads back into separated fastq files?

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