User: pixie@bioinfo

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pixie@bioinfo1.4k
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PhD Student

Posts by pixie@bioinfo

<prev • 224 results • page 1 of 23 • next >
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Answer: A: Self Organizing Maps for RNA-seq data
... Other than Mensur's answer which is great, I managed to get a reply from the authors. Maybe useful if anyone wants to try this out as this is not mentioned anywhere in the R documentation modules.CSV.sheets <- oposSOM:::modules.CSV.sheets environment(modules.CSV.sheets) <- env ...
written 7 weeks ago by pixie@bioinfo1.4k • updated 7 weeks ago by GenoMax94k
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Comment: C: Self Organizing Maps for RNA-seq data
... Thanks for the suggestions. Will try this out. ...
written 7 weeks ago by pixie@bioinfo1.4k
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Self Organizing Maps for RNA-seq data
... Hello, I have normalized reads from RNA-seq data and I am trying to build SOMs using the oposSOM R package. It exports couple of CSV files like K-means, over-expression modules etc. However, I dont see any option to export gene lists for Correlation Cluster, Underexpression Spots. Any one used this ...
rna-seq written 7 weeks ago by pixie@bioinfo1.4k
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Comment: C: Using Deeptool for profile plots
... Thanks so much for the explanations and I went through the paper for the "csaw" suggestion. The data exploration is worth the time. ...
written 7 weeks ago by pixie@bioinfo1.4k
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Comment: C: Using Deeptool for profile plots
... Hello, just to clarify, I should use bedtools makewindows and the chromosome length file to generate a feature file (10kb). Then use featureCounts to extract the matrix which should be used in edgeR or DEseq right ? Thanks ...
written 8 weeks ago by pixie@bioinfo1.4k
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Comment: C: Using Deeptool for profile plots
... Thanks, actually, we were more interested in normalizing across samples, than their differential analysis. I will have a look at the scaling factors you linked! ...
written 8 weeks ago by pixie@bioinfo1.4k
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Using Deeptool for profile plots
... Hello, I have 3 Atac-seq samples which I have normalized across them using MAnorm2 algorithm. (https://github.com/tushiqi/MAnorm2). What I obtained are the different peak regions and the corresponding normalized read counts. I have a list of gene locations of my interest However, for representation ...
deeptools written 8 weeks ago by pixie@bioinfo1.4k
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Issue with Diffreps
... Hello, I am using Diffreps for differential ChIPseq analysis. I keep getting this error which I am unable to fix. The details of the input files and the result files are given below. Any insight is greatly appreciated. ERROR: **median function called for an empty array!** Command: **diffReps.p ...
chip-seq written 8 weeks ago by pixie@bioinfo1.4k
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Ideas Regarding TF regulatory network
... Hello, I am working on tomato with varying levels of heat stress (0h, 1h, and 3h) I have Atac-seq, RNA-seq data (2 replicate each) for all 3 time-points. I also have ChIP-seq data for various Histone marks like H3K27me3, H3K9 Ac, etc. for all 3 time-points I also have I wish to have a TF-regulat ...
network written 10 weeks ago by pixie@bioinfo1.4k
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CUT&RUN analysis pipeline
... Hello, My lab has generated data using the CUT&RUN protocol. Unfortunately, Its single-end data. I tried the CUT&RUN tools and the henipipe tool. Both are for paired end data. Any suggestion how I can analyse these data ? Any idea how to set the parameters in case I use the classical Trim ...
alignment sequencing written 12 weeks ago by pixie@bioinfo1.4k • updated 12 weeks ago by rpolicastro3.1k

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