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User: skjobs0123

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skjobs0123 • 70
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Posts by skjobs0123

<prev • 28 results • page 1 of 3 • next >
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Comment: C: Downstream RNA seq analysis
... You can do a lots of things in down stream process such as gene ontology, pathways analysis, protein protein interaction or you can see how many of the genes are belong to which classes of protein and family. The question is very generic please make precise. What really you want. ...
written 5 weeks ago by skjobs0123 • 70
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Comment: C: Get nucleotide sequence from protein refseq
... Use biodbnet to convert biological ID and then you can fetch from entrez or other site. https://biodbnet-abcc.ncifcrf.gov/db/db2db.php ...
written 12 weeks ago by skjobs0123 • 70
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Comment: C: How to plot gene_names besides CpGs in microarray methylation heatmap?
... Use this code to generate heatmap # Use RColorBrewer color palette names library("RColorBrewer") col <- colorRampPalette(brewer.pal(10, "RdYlBu"))(256) heatmap(df, scale = "none", col = col, RowSideColors = rep(c("blue", "pink"), each = 16), ...
written 12 weeks ago by skjobs0123 • 70
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Comment: C: How to get PPI result quickly using bisogenet in Cytoscape?
... Use HIPPIE database ([http://cbdm-01.zdv.uni-mainz.de/~mschaefer/hippie/][1]) for PPI interaction, Or string. First, mapped Gene ID with these database and then upload table into Cytoscape. Further, you can do whatever you want. [1]: http://cbdm-01.zdv.uni-mainz.de/~mschaefer/hippie/ ...
written 12 weeks ago by skjobs0123 • 70
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Comment: C: query on salmon installation
... then set the PATH in ~/.bashrc ...
written 12 weeks ago by skjobs0123 • 70
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Comment: C: scRNA-seq reduction plot for individual group
... You can use this tutorial [http://cole-trapnell-lab.github.io/monocle-release/monocle3/][1] ...
written 12 weeks ago by skjobs0123 • 70
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Comment: C: Normalization of NGS data generated from different platforms of microRNAs
... Thanks, Samples are not homogeneous like: Sample Condition Machine 1 Control Hiseq 2 Control Hiseq 3 Control Nextseq 4 Control Nextseq 5 Treatment Hiseq 6 Treatment Hiseq 7 Treat ...
written 12 weeks ago by skjobs0123 • 70
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Normalization of NGS data generated from different platforms of microRNAs
... I have read count of microRNAs NGS data generated from different platform such as Illumina NextSeq 500 and HiSeq 2000. Do I need to normalized it before differential expression analysis?. Which is the best of method to normalise data before DEs. I thought the data is generated from two different ma ...
R next-gen rna-seq sequencing written 12 weeks ago by skjobs0123 • 70 • updated 12 weeks ago by i.sudbery ♦ 7.3k
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Comment: C: How to obtain gene symbols from the result list of GEO2R?
... You can use the Biomart in R. https://bioconductor.org/packages/release/bioc/html/biomaRt.html ...
written 3 months ago by skjobs0123 • 70
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Overlap two variable
... I have two variable (A) and (B). I want to cover the maximum alignment overlap using both variables (A) and (B) which is nearly 100. This is my input is like that ID Variable_A Variable_B PDD1 9 42 PDD2 34 60 PDD3 70 ...
assembly sequence R written 3 months ago by skjobs0123 • 70

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Commentator 3 months ago, created a comment with at least 3 up-votes. For A: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
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