User: g.atla

gravatar for g.atla
g.atla0
Reputation:
0
Status:
New User
Location:
Website:
https://www.biostars.o...
Last seen:
8 months, 3 weeks ago
Joined:
1 year, 10 months ago
Email:
g*****@imperial.ac.uk

Posts by g.atla

<prev • 32 results • page 1 of 4 • next >
3
votes
1
answer
405
views
1
answer
How to normalize chromatin and RNA-Seq data together ?
... Dear All, I have chromatin data, from ATAC and other histone marks and RNA-Seq data for same samples. Lets say I have 14 independent samples subjected to ATAC-Seq and RNA-Seq, but at different times, different sequencing centres. Now I want to compare the signal from chromatin data to gene express ...
sva deseq2 combat atac atac-seq written 8 months ago by g.atla0 • updated 8 months ago by Michael Love14k
0
votes
0
answers
186
views
0
answers
Comment: C: dexseq_count.py in shell script
... What is your exact command ? ...
written 13 months ago by g.atla0
0
votes
1
answers
245
views
1
answers
Answer: A: How to manage multiple legends in heatmap_legend_param (ComplexHeatmap) ?
... I understood that the heatmap_legend_param is only for the heatmap and I need to use annotation_legend_param and I can specify nrow and ncol to get the desired format and then I can place them at the bottom using annotation_legend_side = "bottom" ...
written 13 months ago by g.atla0
0
votes
1
answer
245
views
1
answer
How to manage multiple legends in heatmap_legend_param (ComplexHeatmap) ?
... I would like to know how can I manage multiple legends with heatmap_legend_param ?  My annotations looks like head(colData)       purity Center Year  BMI Gender sample1     75 Geneva 2011   20     F sample2    90 Milano 2011 <NA>      F sample3    90  Lille 2011   30      M sample4    80 ...
complexheatmap written 13 months ago by g.atla0
2
votes
1
answer
256
views
1
answer
WGCNA - soft threshold
... I am trying to run WGCNA on variance stailized ran-seq data ( DESeq2 ) on 66 samples ( 33 treated vs 33 untreated ). When I try to chose a soft threshold, I see that the SFT.R.sq does not reach 0.9, which I see in most of the tutorials. According to my understanding, the softPower is chosen when the ...
wgcna written 14 months ago by g.atla0 • updated 14 months ago by Peter Langfelder1.3k
0
votes
1
answers
513
views
1
answers
Comment: C: Incorporate "batch" information for paired-design ?
... So if I want to look if the treatment has different effect on males vs females, I need to create the appropriate model.matrix ? So I should ask the program to give me if there is any difference in the gene expression in males vs females w.r.t treatment ?  It looks complicated to ask "If there is an ...
written 14 months ago by g.atla0
0
votes
1
answer
513
views
1
answer
Incorporate "batch" information for paired-design ?
... I am working with large panel of human tissue cells that are collected from different centres. Its a paired design i.e same sample has treated and untreated rna-seq data. Here is how my colData looks like > colData             purity subjects treat Center Year  BMI Gender  Age sample1_ ...
deseq2 rna-seq batch effect written 14 months ago by g.atla0
0
votes
1
answers
369
views
1
answers
Comment: C: Paired design, normalisation and batch effects.
... The major concern here is not to remove batch effects for DE analysis. The major goal here is to understand the different responses among the samples i.e do all samples show similar behaviour in gene expression changes before and after treatment or are there any subset of samples that show different ...
written 15 months ago by g.atla0
0
votes
1
answers
369
views
1
answers
Comment: C: Paired design, normalisation and batch effects.
... I have updated the post. I have 40 biological replicates ( from different patients ) of the same tissue, with treated and untreated data. I need to check which samples showing similar response and if there are any non responders and samples that are responding differently ( due to stress or the the ...
written 15 months ago by g.atla0
1
vote
1
answer
369
views
1
answer
Paired design, normalisation and batch effects.
... Dear All, I would like to clarify certain doubts and have opinions on the rna-seq data analysis I have been doing. I have RNA-Seq data from paired experiment i.e I have treated and untreated data for the same tissue which is sequenced in the same batch. I have data from 40 different biological sam ...
sva deseq2 rna-seq eda written 15 months ago by g.atla0 • updated 15 months ago by Bernd Klaus470

Latest awards to g.atla

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 117 users visited in the last hour