User: unique379

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unique37950
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Posts by unique379

<prev • 39 results • page 1 of 4 • next >
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Comment: C: Transform duplicate rows into columns.
... Thank you for introducing datamash, i never knew before. I have to install and check if its work for me. But thank you. ...
written 5 months ago by unique37950
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Comment: C: Transform duplicate rows into columns.
... Excellent Thank you. ...
written 5 months ago by unique37950
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Transform duplicate rows into columns.
... Hi all, I would like to make duplicate row lines as columns. So it would be easier to extract repetitive columns as comma separated format. These are transcript isoforms that means one gene has multiple transcript, which I want in one columns by comma separated. Input: 1_58420023_58420024 ...
R bash annotations rna-seq linux written 5 months ago by unique37950 • updated 5 months ago by cpad01125.3k
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Human and Mouse Benchmarking datasets for WGS, WES (variant callling) and RNASeq+differential analysis pipeline.
... Hello all, I am looking for Benchmarking datasets for WGS, WES and RNASeq analysis pipelines. Basically I need fastq, vcf file for WGS and WES and expression count for RNASeq that i can compare with my results. I found GIAB datasets but that contains different technologies which is i dont need, i j ...
dnaseq wes rna-seq wgs written 9 months ago by unique37950
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Need a piece of advice for microbiome data
... Dear folks, I am new to analyze for micro biome data. I am trying to use mothur for my analysis. I have MiSeq paired (fastq) microbiome data. After using contigs and summary.seqs command i need to screen the sequences from my reads. The sumary file look like this: mothur > summary.seqs(fast ...
microbiome miseq written 14 months ago by unique37950
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Designing of model.matrix for batch correction of Time Course data ?
... Dear folks, I would like to correct batch of my time course data but the problem is to design matrix for sva as input. So is there way to design matrix having **two groups (WT and KO) along with four time points (1 month, 3 months, 12 months and 22 months) including their replicates ??** > ...
sva ruvseq rna-seq written 22 months ago by unique37950 • updated 21 months ago by Biostar ♦♦ 20
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Comment: C: why my resultsNames(deseq) is not the same as model.matrix ?
... Thank you Ryan for your kind and efficient answer. I tried with full model then ran deseq wald and LRT test to see the differneces but got very surprising results for the same contrast. How it possible that, Wald Test gave me tags 0 at padj <0.05 while LRT test gave 345 tags at the same level of ...
written 22 months ago by unique37950
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why my resultsNames(deseq) is not the same as model.matrix ?
... Dear all, I have three question about RNASeq analysis of my data using DESeq2. Lets say i have 4 groups and wanna see DE for each combinations of the groups (**By specifying the contrast in results function of DESeq2**). So i used the default setting of DESeq considering intersect/base level (while ...
R sva deseq2 rna-seq written 22 months ago by unique37950 • updated 22 months ago by Devon Ryan79k
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The best test for the two conditional problem.
... Dear all, I am wondering which test is suitable for my case (i have two condition i.e. C (3 replicates) and T (3 replicates)) and what is basically makes difference between "Wald" and "LRT" test implemented in DESeq2. I tested both with my dataset but was surprised when i end up with much differen ...
R bioconductor deseq2 rna-seq written 2.0 years ago by unique37950 • updated 2.0 years ago by Michael Love1.6k
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Comment: C: Any R and bioconductor packages for non parametric test for rna seq count data.
... First of all, I cant use FPKM as i have raw counts instead i used CPM to filter low expressed genes from the beginning (advised by the edgeR itself). ####Keeping tags that have Cutoff (Counts per million) = 1, in at-least half (50%) of the Total sample length.## keep <- rowSums(cpm(DF)> as.n ...
written 2.1 years ago by unique37950

Latest awards to unique379

Popular Question 5 months ago, created a question with more than 1,000 views. For Can't sort gff file ordered by chromosome (ch1,chr2,chr3......chrX).
Popular Question 9 months ago, created a question with more than 1,000 views. For Can't sort gff file ordered by chromosome (ch1,chr2,chr3......chrX).
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Popular Question 18 months ago, created a question with more than 1,000 views. For any tool or R package for integrated analysis of miRNA and mRNA expression data ??
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Popular Question 2.0 years ago, created a question with more than 1,000 views. For miRNA-target network construction packages in R and Bioconductor ??

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