User: anu014

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anu014150
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India
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1 week, 1 day ago
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3 years, 2 months ago
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Posts by anu014

<prev • 135 results • page 1 of 14 • next >
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2 peak files in plotAvgProf2 [ChIPseeker]
... Hello Biostars!, Can someone tell me how to plot 2 peak files in a single plot using plotAvgProf2. I was using below command but it gave me just one sample: plotAvgProf2(c(peak2,peak3), TxDb=txdb, upstream=3000, downstream=3000,weightCol="fold_enrichment", xlab="Genomic Region (5'->3')", yl ...
R bioconductor chip-seq chipseeker written 8 days ago by anu014150 • updated 7 days ago by zx87545.4k
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Comment: C: Applying Steiner minimal tree algorithm in Cytoscape
... Thanks a lot Gary! It sounds quite promising. I installed ANAT app in Cytoscape. But the 'New Sub-network' option doesn't work somehow for me.. It starts like - 'Retrieving available networks.. Network Problem'. How this can be fixed? Same for 'New Background Network' option. ...
written 23 days ago by anu014150
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Crosstalk between KEGG pathways
... Hello Biostars, I used clusterProfiler for KEGG pathway enrichment. Now I want to do crosstalk over them. I utilized jaccard coefficient in order to measure overlap between the pathways. But my problem is that from clusterProfiler I'm getting many irrelevant pathway enrichment too (my gene entries ...
gene genome sequence kegg written 7 weeks ago by anu014150
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Vertices name in steinertree [R]
... Hello all, Can anyone tell me how to retain the name of vertices in steinertree package (R)? Below is the code I used. The final object SP (igraph object) is the one that is showing node names as 1,2,3.. library(igraph) library(SteinerNet) a <- read.table("inte ...
gene ppi graph written 10 weeks ago by anu014150
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Applying Steiner minimal tree algorithm in Cytoscape
... Hello Biostars! It's been quite a long time since I posted here. I hope you all are doing great. This time I need your help in finding sub-network in Protein-Protein Interaction networks (from STRINGdb) using steiner minimal tree algorithm. For this, I want a plugin that I can install directly on ...
gene ppi cytoscape written 11 weeks ago by anu014150 • updated 9 weeks ago by gary.bader20
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Neoantigen prediction Tools
... Hello everyone! Can anyone suggest me some tools for neoantigen prediction in Whole exome sequencing data? ...
next-gen alignment snp written 3 months ago by anu014150 • updated 3 months ago by Chris Miller20k
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Comment: C: Using wig2array from iSeeRNA
... My problem is partially solved. As right now I wanted to work on mm10. But how to do the same for hg38? iSeeRNA just has in-bulit files for hg19/mm9/mm10. ...
written 4 months ago by anu014150
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Using wig2array from iSeeRNA
... Hello Biostars, I want to identify lincRNAs from RNA-Seq data. For this purpose, first I ran cufflinks which gave me GTF to enter into iSeeRNA which in turn asked me to enter .conf file. For .conf file, I need to have .array file also. So can anyone tell me how to create .array file using wig2arr ...
genome next-gen rna-seq written 4 months ago by anu014150 • updated 7 weeks ago by hellosunking0
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Comment: C: Cytoscape's plugin 'stringApp' error
... Yes, that's it! Thanks xanderpico. ...
written 4 months ago by anu014150
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Cytoscape's plugin 'stringApp' error
... Hello Biostars, Today, I'm doing network analysis using Cytoscape. I installed 'stringApp' plugin for getting STRINGDb network. After adding 'gene symbol' list in it, I ran strinApp. As a result, got node, edge and network text files. The node file I got contains those genes also which I never e ...
software error gene cytoscape written 4 months ago by anu014150 • updated 4 months ago by xanderpico150

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