User: sysbiocoder

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sysbiocoder180
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Posts by sysbiocoder

<prev • 27 results • page 1 of 3 • next >
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Answer: A: Loess Normalization And Scale Issues
... You can also impute the values. There are several options. Please go through this tutorial http://r-statistics.co/Missing-Value-Treatment-With-R.html ...
written 15 months ago by sysbiocoder180
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Comment: C: How to draw venn diagram for two CNV lists?
... 10 CNVs in list1 overlaps with 20 cnvs in list2 It means there are duplicates in list. While drawing Venn we consider only unique values. Hope I answered your question ...
written 15 months ago by sysbiocoder180
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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 21 months ago by sysbiocoder180
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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 2.3 years ago by sysbiocoder180 • updated 2.3 years ago by kristoffer.vittingseerup2.9k
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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 2.3 years ago by sysbiocoder180
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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 2.9 years ago by sysbiocoder180
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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 2.9 years ago by sysbiocoder180
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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 2.9 years ago by sysbiocoder180
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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 2.9 years ago by sysbiocoder180
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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 2.9 years ago by sysbiocoder180

Latest awards to sysbiocoder

Scholar 2.9 years ago, created an answer that has been accepted. For A: Comparing 2 different sets of RNAseq data - correlation
Scholar 2.9 years ago, created an answer that has been accepted. For A: Comparing 2 different sets of RNAseq data - correlation
Commentator 2.9 years ago, created a comment with at least 3 up-votes. For C: rna seq bowtie couldn't find index files

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