User: Hushus

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Hushus 20
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Molecular turned binary 

Posts by Hushus

<prev • 21 results • page 1 of 3 • next >
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Overlapping Bedgraph - Microarray ChIP to BigWig for Clustering analysis
... Good afternoon everyone, I've been playing around with publicly available ChIP-seq datasets and have been clustering regions, producing heatmaps, and all that fun stuff. Now, my data analysis hinges on a set of ChIP-chip (on microarray) data and Im having trouble interpreting the data deposited to ...
bedgraph chip bigwig microarray heatmap written 11 months ago by Hushus 20
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Comment: A: How to continue processing Hi-C reads
... I editted the file to the following to be put into juicebox: str1 - ch1 - pos1 - frag1 (all are 0) str2 - ch2 - pos2 - frag2 (all are 1) Am i in the right direction or because these reads are all ready normalized and binned that I dont need to do this step? ...
written 2.5 years ago by Hushus 20
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How to continue processing Hi-C reads
... Hello all, I am new to Hi-C data processing and am wondering what to do from here. I am sort of familiar with Juicebox and the hifive manipulation in Galaxy but I really need advice. So I have the following information: chromosome_1 | strand_1 | position_1| DistanceClosestRestrictionSite_1 | ...
hi-c conformation chromatin chromatin capture written 2.5 years ago by Hushus 20
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Answer: A: Looking to get PATTERN CLUSTERING of gene expression data with multiple time poi
... **ANSWER**: DOWNLOAD MeV SOFTWARE USE K-MEANS CLUSTERING, PEARSON. YOU GET THE FOLLOWING: ![enter image description here][1] [1]: https://image.ibb.co/b9gGvG/Yoyo.jpg GOOD ENOUGH FOR ME. ...
written 2.5 years ago by Hushus 20
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Comment: C: Looking to get PATTERN CLUSTERING of gene expression data with multiple time poi
... Oooo thank you for your detailed input. I will definitely try this out. How would you plot the results? ...
written 2.5 years ago by Hushus 20
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Looking to get PATTERN CLUSTERING of gene expression data with multiple time points
... Hello all, This is the 3rd thread concerning this issue and we have made steady progress. I sincerely appreciate the inputs of cpad0112 and h.mon for their efforts Have: * RNA expression data for 12 time points, 1 replicate * List of genes of interest and their expression data http://m.uploade ...
cluster pattern rna-seq expression written 2.5 years ago by Hushus 20
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Comment: C: Cannot get result from TIMECOURSE (R PROGRAM)
... Hmm must be so... Do you know of another way of producing a similar plot as the one I recently posted? Im gonna start a new thread on this ...
written 2.5 years ago by Hushus 20
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Comment: C: Cannot get result from TIMECOURSE (R PROGRAM)
... 12 time points x 1 experiment. [I have a list of 100 genes, this is just a sample] So I dont expect a plot from plotProfile with my results? How can I get a clustered image like this one: ![enter image description here][1] [1]: https://warwick.ac.uk/alumni/services/eportfolios/hrrgak/project ...
written 2.5 years ago by Hushus 20
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Answer: A: Cannot get result from TIMECOURSE (R PROGRAM)
... I only have 1 biological condition and only 1 replicate. Do you need multiple replicates? Here is the data: http://m.uploadedit.com/bbtc/1512924884525.txt I used your code and got the following. "out1" is giving me the exact same thing and when I try to plot it, nothing shows. The plot image is ...
written 2.5 years ago by Hushus 20
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Cannot get result from TIMECOURSE (R PROGRAM)
... [This is a follow-up to my previous post] Hello world, I have a set of genes whose RNA expression is catalogued in development (FlyBase temporal RNA-seq). I want to find which genes go up and down at time point "A_07" and possibly cluster genes to their patterns also. I put this into R and use ...
pattern rna timecourse development written 2.5 years ago by Hushus 20

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