User: mbk0asis

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mbk0asis530
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Posts by mbk0asis

<prev • 141 results • page 2 of 15 • next >
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Comment: C: fGSEA result to csv
... Thnanks! It worked!! ...
written 5 months ago by mbk0asis530
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6 follow
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fGSEA result to csv
... Hi, all! I've obtained the enriched GO BP terms using fGSEA in R as shown below. 1: GO_POSITIVE_REGULATION_OF_VIRAL_TRANSCRIPTION 0.020378457 0.08797654 0.4748196 1.5113374 13 41 TFAP4,NELFCD,POLR2H,POLR2D,NELFA,DHX9,... 2: GO_CARDIAC_CHA ...
fgsea rna-seq gsea written 5 months ago by mbk0asis530 • updated 5 months ago by alserg440
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Comment: C: WGCNA package in R: dendogram plot error
... How can I extract gene lists from blocks and dendros? ...
written 6 months ago by mbk0asis530
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WGCNA blockwiseConsensusModules : number of colors and objects in dendrogram don't match
... Hi. I'm running WGCNA to find consensus modules between two experiments. I'm stuck at 'plotDendroAndColor' step due to the mismatch of the number of 'consTree' and 'moduleColors' as shown below. As a result, the plot showed only the dendrogram but no colored modules. > length(moduleColor ...
wgcna blockwiseconsensusmodules written 6 months ago by mbk0asis530
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Comment: C: Joining vs merging paired ended reads
... Check out ['PANDAseq'][1]. "PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence." You can also find many other similar tools on the web. [1]: https://github.com/neufeld/pandaseq ...
written 6 months ago by mbk0asis530
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Comment: C: deepTools cluster information?
... As Devon Ryan mentioned, gene names won't be appeared in the result. You can annotate the regions with gene names using 'bedtools intersect'. ...
written 6 months ago by mbk0asis530
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Comment: C: gdc-client download: ERROR: Max retries exceeded
... Try 'TCGAbiolinks'! https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html ...
written 10 months ago by mbk0asis530
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Comment: C: How to speed up trimming using trim galorer
... Much better! Thanks~ ...
written 16 months ago by mbk0asis530
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Answer: A: How to speed up trimming using trim galorer
... Use GNU Parallel! Your 'for-loop' code processes one sample at a time. (it waits until one sample is finished and starts next.) Use 'parallel' to process multiple samples simultaneously! If you have reads like this; sample1.R1.fq.gz sample1.R2.fq.gz sample2.R1.fq.gz sample2.R2.f ...
written 16 months ago by mbk0asis530
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Comment: C: How to calculate read frequency from read counts for each gene in all samples al
... I'm not sure what exactly you want, but I assume you don't know how to fix a field using '$' sign. If so, check this cite. [https://www.excel-easy.com/functions/cell-references.html][1] But excel is not efficient to handle a larger dataset. Use R or something similar. They are much better! [1]: ...
written 20 months ago by mbk0asis530

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