User: pthom010

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pthom0100
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Posts by pthom010

<prev • 32 results • page 1 of 4 • next >
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Comment: C: GO Term Analysis
... Thanks. A bit confused on the padj point. I was looking on the gprofiler page and don't see anywhere to input background genes. I have a set of differentially expressed TFs clustered into groups. Would you recommend my background be all TFs that are non NA or just all non NA genes? Thanks for the re ...
written 5 weeks ago by pthom0100
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GO Term Analysis
... I am conducting an RNA seq analysis in R using DESeq2. I have a few sets of differentially expressed genes from a de novo organism and have the TAIR equivalents. I was wondering if there is a program in R/R Studio I can use to do GO term enrichment analysis with the TAIR locus ID numbers (or the nuc ...
R rna-seq go annotation written 5 weeks ago by pthom0100
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Comment: C: DESeq2 and DEXSeq
... Essentially, I have two unique individuals we did a time course on and I wanted to look at differential exon usage and gene expression. So I want to do both things but was wondering if there was a program that could incorporate my DESeq and DEXSeq data to enhance my analysis. ...
written 6 weeks ago by pthom0100
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DESeq2 and DEXSeq
... I have reads from 30 samples that I de novo assembled with Trinity and started using the assembly in a differential expression analysis in DESeq2. However, I also have supertranscripts assembled by Trinity and recently learned about DEXSeq. Would it be redundant to finish my DESeq analysis and then ...
dexseq trinity deseq2 written 6 weeks ago by pthom0100
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Comment: C: Retrieve Clusters From ComplexHeatmap
... This worked. Thanks! ...
written 7 weeks ago by pthom0100
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Retrieve Clusters From ComplexHeatmap
... I made a heatmap with the following data (the actual table has 240 rows): tf.log 0-dpi 1-dpi 7-dpi 14-dpi 22-dpi TRINITY_DN0_c0_g1_i2 1.27584408 0.5872404 1.780178 1.414362 1.53341851 TRINITY_DN10214_c0_g1_i2 -2.34774378 -2 ...
R complexheatmap written 7 weeks ago by pthom0100 • updated 7 weeks ago by ATpoint41k
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TAIR Gene Symbols
... Does anybody know where I can acquire a table of TAIR Gene Symbols? What I have is a file with TAIR locus IDs and I would like to get the gene symbols that correspond with them. I have some coding experience in Linux and R so if there is a solution based in either one of those resources, that would ...
arabidopsis genetics genomics written 8 weeks ago by pthom0100 • updated 8 weeks ago by genomax92k
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Convert Loci to Gene Names?
... I have a series of Medicago truncatula loci (Medtr3g093830.1, Medtr4g100630.1) and I wanted to get their gene names (ex. *PR2* or *UBQ5*). I've been looking around with no success. Would anybody know about a resource I can use to retrieve these names for the respective loci? I have coding experience ...
gene annotation rna-seq written 9 weeks ago by pthom0100 • updated 9 weeks ago by Fatima830
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(Closed) K Means Clustering Two Matrices for ComplexHeatmap
... I have a csv file with the log2 scores of eight different timepoints. The header of the table looks like this: head(templogs) SB SC SD SE TRINITY_DN1001_c0_g1_i1 -0.5638283 -1.2861425 -0.8790812 -1.9667007 TRINITY_DN1001_c0_ ...
R rna-seq complexheatmap written 10 weeks ago by pthom0100
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Add Both Legends to a Plot
... ![My Attempt][1] I have a plot that I have made counting the number of genes over a period of time in two samples. I would like to plot both sets of numbers in a waterfall chart. I am able to get the chart but I have difficulty getting both legends to show up. I have the following tables: deg. ...
R written 11 weeks ago by pthom0100 • updated 11 weeks ago by antonioggsousa1.5k

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Popular Question 2.5 years ago, created a question with more than 1,000 views. For Align Reads from PacBio

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