Showing : RNA-SEQ • reset
5
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7
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239
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Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 3 days ago by 47k • written 3 days ago by ▴ 10
0
votes
3
replies
195
views
Is the gene-specific PCR efficiency a serious concern for intrasample comparisons in RNA-Seq?
RNA-Seq normalization PCR_efficiency bias intrasample_comparison
updated 18 days ago by 62k • written 18 days ago by • 0
0
votes
3
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218
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Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 18 days ago by 62k • written 18 days ago by • 0
1
vote
1
reply
164
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 6 weeks ago by ★ 2.8k • written 6 weeks ago by • 0
0
votes
1
reply
131
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 9 weeks ago by 62k • written 9 weeks ago by • 0
2
votes
2
replies
198
views
Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 9 weeks ago by ★ 2.8k • written 9 weeks ago by • 0
0
votes
1
reply
155
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
3 months ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
283
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 6 months ago by 40k • written 6 months ago by • 0
5
votes
9
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916
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GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
10 months ago Yang Shi ▴ 10
2
votes
2
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493
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
10 months ago Yang Shi ▴ 10
0
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0
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440
views
Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
10 months ago eolson • 0
2
votes
2
replies
406
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 10 months ago by 47k • written 10 months ago by • 0
0
votes
2
replies
770
views
Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 17 days ago by • 0 • written 2.6 years ago by • 0
4
votes
8
replies
1.2k
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
updated 3 months ago by 62k • written 3.0 years ago by ▴ 30
1
vote
4
replies
544
views
Nested paired design with covariates in limma
RNA-seq Nested paired design limma
updated 3 months ago by 47k • written 3.2 years ago by • 0
4
votes
6
replies
4.5k
views
strange results with featureCounts
RNA-seq featureCounts total RNA
updated 7 months ago by ▴ 20 • written 5.0 years ago by ▴ 10
16 results • Page 1 of 1
Recent ...
Replies
Comment: Recount3: PCR duplicates by ATpoint ★ 2.8k
The maintainers might answer specifically for recount3, but in general PCR (or any) duplication is not removed in RNA-seq (or targeted assa…
Comment: Normalized counts from LRT or Wald test? by sneha108ss • 0
That is great to know! Thank you
Comment: Installing densvis on a Singularity container by alan.ocallaghan ▴ 120
Do you have gfortran installed? eg [this installation package][1] [1]: https://github.com/fxcoudert/gfortran-for-macOS
Comment: Installing densvis on a Singularity container by azp0136 • 0
I get the same error when I try to install densvis in R with `BiocManager::install("densvis")` and I have no idea how to solve this problem…
Comment: Error in DGEList(counts = cnt, group = group) : non-numeric values found in c by Luis • 0
Thank you so much!
Votes
How to create "trait data" file for WGCNA
Comment: Visualization of negative log CPM values
Answer: Extracting fitted expression matrix from Limma
Answer: DESeq2 or edgeR for Presence and Absence of Proteins
Comment: Visualization of negative log CPM values
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