User: aiswaryabioinfo

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Posts by aiswaryabioinfo

<prev • 16 results • page 1 of 2 • next >
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Comment: C: How to draw a chromosome graph with only selected genes marked in it
... Thank you sir, this will really help me. I only want to make the map of one single chromosome with highlighting certain specific genes in that chromosome. I will try your suggestions. ...
written 3 months ago by aiswaryabioinfo20
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Comment: C: How to draw a chromosome graph with only selected genes marked in it
... I have checked karyoploteR but it is not serving my purpose my data is like this gene chromosome start end gene1 4 20 3000 gene2 4 4000 5000 gene3 4 6000 7000 I want to mark this genes in corresponding chromosome and make a gra ...
written 3 months ago by aiswaryabioinfo20 • updated 3 months ago by RamRS24k
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How to draw a chromosome graph with only selected genes marked in it
... Dear all, I need to draw a linear chromosome graph for a specific chromosome with marking selected genes segments instead of the whole chromosome. My chromosome is having a size of 135.06mb (genbank file size: 181mb) I could find online tools like "ogdraw" which are specific for organelles like ch ...
genome chromosome visualization map tool written 3 months ago by aiswaryabioinfo20 • updated 3 months ago by bernatgel2.1k
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Comment: C: DESeq2 compare all levels using wald and lrt test
... Hi Devon, I got the error as typo Is it necessary to use lfcshrink() in all_vs_all design comparison. Will it affect in identification of significant genes? What affect lfcshrink () will have in the expression values of genes? I tried the all_vs_all design comparison in DESeq2 (Version 2.11.40.2) ...
written 3 months ago by aiswaryabioinfo20
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DESeq : base mean value are same for all genes in all the three combinations in compare all levels design
... My RNA-seq dataset consist of Resis_treated (1st day, 3rd day and 7th day) samples taken under 3 time point with 2 replicated for each time point. I have a condition with 3 levels (day1, day3, day7). I used HTseq-count to get the read counts. I am trying to get the DEGs between Day3VsDay1, Day7VsDa ...
R deseq2 log2fc base mean written 3 months ago by aiswaryabioinfo20 • updated 3 months ago by h.mon27k
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Comment: C: DESeq2 compare all levels using wald and lrt test
... After running the code, I tried to contrast day7_Vs_Day3 data. But it showed an error as follows day73 <- lfcShrink(dds, contrast=c("condition", "day7", "day3")) Error in cleanContrast(object, contrast, expanded = isExpanded, listValues = listValues, : day7 and day3 should be levels of cond ...
written 3 months ago by aiswaryabioinfo20
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Comment: C: DESeq2 compare all levels using wald and lrt test
... Thank you sir for your help ...
written 3 months ago by aiswaryabioinfo20
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Comment: C: DESeq2 compare all levels using wald and lrt test
... What is the difference in using LRT in this context (All_vs_all comparisons) ...
written 3 months ago by aiswaryabioinfo20
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Comment: C: DESeq2 compare all levels using wald and lrt test
... Hi Devon, Will I get the condition_Day7_vs_Day3 combinations through the following command day73 <- results(dds, contrast=c("condition", "day7", "day3")) day73 <- lfcShrink(dds, contrast=c("condition", "day3", "day3"), res=day73)` #(Use lfcShrink() with the contrast= option 3 times.) ...
written 3 months ago by aiswaryabioinfo20 • updated 3 months ago by Devon Ryan92k
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DESeq2 compare all levels using wald and lrt test
... I am currently working in plant pathogen interaction and is trying to make a gene co-expression network using RNA-seq data. I used HTseq-count to get the read counts. My dataset consist of Resis_treated (1st day, 3rd day and 7th day) samples taken under 3 time point with 2 replicated for each time ...
R deseq2 differential expression written 3 months ago by aiswaryabioinfo20 • updated 3 months ago by Devon Ryan92k

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