User: Abhishek Pratap

gravatar for Abhishek Pratap
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Posts by Abhishek Pratap

<prev • 21 results • page 1 of 3 • next >
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project tophits onto a public PPI (protein-protein interaction) dbase to identify neighbours
... I want to project the identified tophits genes(RNA-Seq) and proteins(proteomics MS/MS) onto a network of protein-protein interaction dbase and zoom into regions that are 1-2 degree away from our search proteins.  I am pretty positive this should be a solved problem in BioC space. Before I spend too ...
network analysis igraph ppi written 17 months ago by Abhishek Pratap170
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intansv: error reading delly output into R
... Dear Wen I am getting the following error when I trying to load delly output run together on 20 samples.    delly <- readDelly(dataDir=data_dir, regSizeLowerCutoff=100,                 regSizeUpperCutoff=10000000, readsSupport=5,           method="DELLY", pass=TRUE, minMappingQuality=20)   ...
sv delly intansv written 2.5 years ago by Abhishek Pratap170 • updated 2.5 years ago by Dan Tenenbaum ♦♦ 8.2k
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Visualizing Structural variants
... Hi group   Just wanted to learn from your experience on few select visualizing structural variants we found in our long insert libraries for ~20 samples. The goal is not to do global picture coz it get messy/uninformative pretty soon but to zoom in on few select genes. Any tools / examples where ...
visualization sv written 2.6 years ago by Abhishek Pratap170 • updated 2.6 years ago by Vincent J. Carey, Jr.6.2k
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ggbio: examples of overlaying multiple assay datasets
... Hi Tengfei and others Just wondering if you know of some code based examples where people have used ggbio based circular plots for overlaying different expression based datasets. I have RNA, miRNA and methylation datasets that I would love to present it users in a single plot using some sort of a ...
visualization ggbio written 3.2 years ago by Abhishek Pratap170 • updated 3.2 years ago by Panagiotis Moulos30
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WGCNA: help with comparing multiple GEO studies
... Hi Steve and Peter My basic goal here is to study genetic similarities(if any) between a group of GEO studies. I have downloaded about 6-8 studies and as one would expect there is heterogeneity amongst them (diff platform, versions, study sizes(15 - 120 samples) etc). After initial step of normaliz ...
written 3.2 years ago by Abhishek Pratap170 • updated 3.2 years ago by Peter Langfelder1.3k
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Comment: C: ggvis: interactive heatmaps
... Hi Steve I should have mentioned that I am using shiny interface to give user some options to do data filtering. I am interested in finding if there are tools that can help me get tootip and brushing capability. What I mean by brushing is to select subset of the data from the heatmap directly and t ...
written 3.3 years ago by Abhishek Pratap170
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ggvis: interactive heatmaps
... Just wondering if someone knows or have come up with an implementation of interactive heatmap using ggvis. Any other tools/pointers welcome too. Cheers! -Abhi ...
written 3.3 years ago by Abhishek Pratap170 • updated 3.3 years ago by Ying Chen110
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Comment: C: processing Illumina HT12v4.0 expression data from GEO
... Thanks Sean. I guess if I need to dig deeper I will have to follow up with authors. For now I will just explore the normalized data that is present at GEO. Cheers! -Abhi On Wed, Jul 23, 2014 at 9:06 AM, Sean Davis wrote: > I think the file named: > > GSE58037_meningiomas.raw.txt.gz > ...
written 3.3 years ago by Abhishek Pratap170
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Comment: C: processing Illumina HT12v4.0 expression data from GEO
... Hi Sean I did download and open the files under raw data and strangely enough they have two files which seem like annotation for the Illumina probes. http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE58037&format=file&fil e=GSE58037%5Fmeningiomas%2Eraw%2Etxt%2Egz -A On Wed, Jul 23, 2014 a ...
written 3.3 years ago by Abhishek Pratap170
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Comment: C: processing Illumina HT12v4.0 expression data from GEO
... Hi Sean Thanks for the details. I actually was wondering if I can get the raw data so I can do my own normalization. For example in the case of affy based GEO studies I normally see the raw CEL files also present which can be used with fRMA for producing normalized data. In this specific study htt ...
written 3.3 years ago by Abhishek Pratap170

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Popular Question 17 months ago, created a question with more than 1,000 views. For ggvis: interactive heatmaps

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