User: jjrin

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jjrin10
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1 month, 3 weeks ago
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2 years, 5 months ago
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l********@yahoo.com

Posts by jjrin

<prev • 36 results • page 1 of 4 • next >
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CLC not outputting or showing table from Fisher's Exact Test
... Hello, we are using Fisher's exact test on a reference file (b2g file) and a selection ID list. While the fisher's exact test finishes and says done, there is no table or file that is outputted, saved, or opened. The test log also does not show any errors when running, are there any other problems t ...
fisher's exact test clc fisher blast2go rna-seq written 7 weeks ago by jjrin10 • updated 4 weeks ago by Jonathanjacobs240
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Tracing back files used in CLC Genomics?
... Hello, I did an RNA-Seq Analysis a while ago on CLC genomics workbench 10 and I am trying to figure out which version of reference files I used. Is there anyway to trace back the original fasta and genome files, or commands I used? Thanks for your help! ...
clc fisher blast2go blast rna-seq written 7 weeks ago by jjrin10 • updated 3 days ago by Biostar ♦♦ 20
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Comment: C: Prefiltering gene lists and DESeq
... Thanks for your reply! The problem is that my gene lists are already prefiltered because I did batch correction on them (using sva seq) which requires prefiltering. Therefore all of my gene lists are different lengths since I batch corrected them in subsets, one treatment with one master control gr ...
written 20 months ago by jjrin10
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Prefiltering gene lists and DESeq
... Hello, I am doing DESeq on my RNA-Seq data. However, I have filtered my conditions individually based on the replicates within each condition. Basically, I have 5 conditions with 5 replicates. I filtered each condition based on the rowmeans of the replicates (5 and above reads are kept). However, no ...
R deseq rna-seq written 20 months ago by jjrin10 • updated 20 months ago by h.mon29k
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Comment: C: R ggplot Align Y-Axis on multiple graphs
... Oh my you're right, I use the same username there and I thought I was posting there. Won't do that again. ...
written 22 months ago by jjrin10
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R ggplot Align Y-Axis on multiple graphs
... Hello I used ggarrange to create this plot, and I would like to align the y axis so that the y axis is the same throughout all graphs instead of being off center. Thank you. ![Misaligned y axis][1] [1]: https://image.ibb.co/k3s6YH/image.png ...
R ggplot2 ggarrange written 22 months ago by jjrin10 • updated 4 months ago by Biostar ♦♦ 20
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Can't make sva comparison despite very distinct batch effects
... I continuously receive this error when I try to run sva with my count data R code for sva: # Loading all variables library(sva) dat <- dds_matrix idx <- rowMeans(dat) > 1 dat <- dat[idx,] mod <- model.matrix(~batch, colData(dds)) mod0 <- model.mat ...
sva factors batch effect written 22 months ago by jjrin10
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Plotting a PCA Plot from SVASeq results
... Hello, I used SVASeq to remove batch effects in my data set. I have run SVASeq and gotten 8 surrogate variables and all of the covariates necessary for my conditions. How would I plot a more detailed PCA plot rather than the give plot svseq function that is used in the vignette? I am thinking of s ...
pca plot sva batch effects svaseq ruvseq written 22 months ago by jjrin10
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Using Mann-Whitney U Test to compare replicates
... Hello, I have several replicates of a certain variable (at least 5). I would like to compare these distributions to see how similar they are with each other. I have TPMs as a measurement as well as counts (if necessary). They are not normally distributed and I read that the Mann-Whitney U-Test is an ...
R rna-seq statistics written 2.1 years ago by jjrin10 • updated 2.1 years ago by Jean-Karim Heriche21k
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Salmon, Getting New TPM from new, updated NumReads
... Hello, I have recently normalized my read counts (NumReads in Salmon output) and I would like to get the new updated TPMs using these Numreads counts. Is there a method I could go around doing this? The effective length and length would be the same regardless. I have all of the same data available, ...
numreads alignment salmon written 2.1 years ago by jjrin10

Latest awards to jjrin

Popular Question 20 months ago, created a question with more than 1,000 views. For R ggplot Align Y-Axis on multiple graphs
Popular Question 20 months ago, created a question with more than 1,000 views. For Plotting a PCA Plot from SVASeq results
Popular Question 20 months ago, created a question with more than 1,000 views. For Can't make sva comparison despite very distinct batch effects
Popular Question 20 months ago, created a question with more than 1,000 views. For Using Mann-Whitney U Test to compare replicates
Popular Question 20 months ago, created a question with more than 1,000 views. For Gffread error: Error (GFaSeqGet): subsequence cannot be larger than...
Popular Question 20 months ago, created a question with more than 1,000 views. For Lack of 5' UTR in genome?
Popular Question 20 months ago, created a question with more than 1,000 views. For Remove the last few bases from fasta sequences

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