User: sysbiocoder

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sysbiocoder150
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Posts by sysbiocoder

<prev • 22 results • page 1 of 3 • next >
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Answer: A: Alternatives to Gene Set Enrichment Analysis dedicated for single samples
... There is an option in GSEA where you can rank genes based on fold change Check below post https://www.biostars.org/p/150586/ ...
written 4 weeks ago by sysbiocoder150
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Comment: A: "inSilicoDB" package in R can't access to webservice
... Not an expert though, try replacing https with http, sometimes it solves the issue ...
written 4 weeks ago by sysbiocoder150
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Answer: A: How to perform Fisher's exact test between two gene lists for a particular gene
... You can use Gene Overlap package in R https://bioconductor.org/packages/release/bioc/html/GeneOverlap.html ...
written 4 weeks ago by sysbiocoder150
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Comment: C: How to Download RNAseq-Clinical Follow up data of BRCA
... TCGA has both open access and controlled access data To get controlled access data you have to request permission https://dbgap.ncbi.nlm.nih.gov/aa/dbgap_request_process.pdf ...
written 4 weeks ago by sysbiocoder150
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Answer: A: How to Download RNAseq-Clinical Follow up data of BRCA
... Are you talking about TCGA, then you can get from https://gdc-portal.nci.nih.gov/. ...
written 5 weeks ago by sysbiocoder150
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Answer: A: Request to BioMart web service failed. Verify if you are still connected to the
... I don't see any mistake. Are you connected to internet ...
written 6 weeks ago by sysbiocoder150
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Comment: C: How are rat genome's CpG islands calculated?
... https://genome.ucsc.edu/goldenpath/gbdDescriptionsOld.html#CpGIslandExt ...
written 6 weeks ago by sysbiocoder150
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Answer: A: survival analysis using R
... Try this plot(try_surv,**mark.time=TRUE**, xlab="Survival", ylab="Survival Probability") ...
written 6 weeks ago by sysbiocoder150
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Answer: A: Comparing 2 different sets of RNAseq data - correlation
... Check this package for normalization http://bioconductor.org/packages/release/bioc/html/sva.html For correlation analysis, there are many packages available, you can use corrplot https://cran.r-project.org/web/packages/corrplot/vignettes/corrplot-intro.html ...
written 6 weeks ago by sysbiocoder150
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Answer: A: Converting .fasta files to .gff3 files
... 1. Convert fasta to BED first Check this https://www.biostars.org/p/15476/ for that 2. use gff-tools (http://www.raetschlab.org/suppl/gff-tools) to convert BED to gff3 ...
written 6 weeks ago by sysbiocoder150

Latest awards to sysbiocoder

Scholar 6 weeks ago, created an answer that has been accepted. For A: Comparing 2 different sets of RNAseq data - correlation
Scholar 7 weeks ago, created an answer that has been accepted. For A: Comparing 2 different sets of RNAseq data - correlation
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: rna seq bowtie couldn't find index files

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