User: sysbiocoder

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sysbiocoder170
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Posts by sysbiocoder

<prev • 25 results • page 1 of 3 • next >
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Answer: A: Quantitative comparison of two different ChIP-seq data from same conditions
... makeUCSCfile function in Homer provides option for normalizing the samples http://homer.ucsd.edu/homer/ngs/ucsc.html ...
written 5 months ago by sysbiocoder170
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Enhancer distance cutoff
... How far can be the enhancer peaks (H3K27ac) associated with TSS of the protein coding gene. As enhancer can act at long distance, I want to concentrate on Cis-acting enhancers and use it for Geneset enrichment analysis ...
enhancer chip-seq written 11 months ago by sysbiocoder170 • updated 11 months ago by kristoffer.vittingseerup470
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Answer: A: Accepted Workflows for Strongly Ontology/Pathway-Driven Analyses of RNA-seq Data
... Use the differentially expressed genes to determine the biological significant pathways with GeneSCF http://genescf.kandurilab.org/ Check if the pathway of interest is enriched, you cannot just use only selected genes for enrichment analysis ...
written 11 months ago by sysbiocoder170
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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 19 months ago by sysbiocoder170
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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 19 months ago by sysbiocoder170
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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 19 months ago by sysbiocoder170
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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 19 months ago by sysbiocoder170
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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 19 months ago by sysbiocoder170
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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 19 months ago by sysbiocoder170
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Comment: C: How are rat genome's CpG islands calculated?
... https://genome.ucsc.edu/goldenpath/gbdDescriptionsOld.html#CpGIslandExt ...
written 19 months ago by sysbiocoder170

Latest awards to sysbiocoder

Scholar 19 months ago, created an answer that has been accepted. For A: Comparing 2 different sets of RNAseq data - correlation
Scholar 19 months ago, created an answer that has been accepted. For A: Comparing 2 different sets of RNAseq data - correlation
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: rna seq bowtie couldn't find index files

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