Showing : CQN • reset
0
votes
9
replies
2.0k
views
normalization method & dispersion estimation RNA-seq data
Normalization edgeR cqn Normalization edgeR cqn
updated 11.4 years ago by 50k • written 11.4 years ago by ★ 13k
0
votes
3
replies
1.8k
views
Voom and CQN input
Normalization limma cqn Normalization limma cqn
updated 10.4 years ago by 50k • written 10.4 years ago by ▴ 30
0
votes
5
replies
3.1k
views
DESeq2
Normalization Classification Clustering DESeq cqn DESeq2 Normalization Classification cqn
updated 11.1 years ago by 41k • written 11.1 years ago by ★ 13k
0
votes
9
replies
2.1k
views
DESeq2 stuck running
cqn DESeq2 cqn DESeq2
updated 9.9 years ago by 41k • written 10.0 years ago by ★ 13k
0
votes
7
replies
2.2k
views
Getting counts for previously undetected transcripts and genes with easyRNASeq: comparison to Cufflinks
RNASeq Annotation Cancer edgeR cqn easyRNASeq RNASeq Annotation Cancer edgeR cqn
updated 11.4 years ago by ★ 1.2k • written 11.4 years ago by ★ 2.0k
2
votes
2
replies
1.2k
views
CQN and EdgeR Library Size for Normalization
CQN atac-seq normalization edgeR
5.9 years ago shankasal • 0
3
votes
4
replies
4.1k
views
What is the easiest way to make the GC content and length matrix for package cqn?
RNASeq edgeR cqn RNASeq edgeR cqn
updated 10.0 years ago by 25k • written 10.0 years ago by ▴ 350
0
votes
1
reply
1.9k
views
using offsets from EDASeq and cqn for edgeR
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
11.1 years ago Kasper Daniel Hansen ★ 6.5k
4
votes
2
replies
2.2k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw chip-seq normalization edger cqn
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 20
9
votes
4
replies
3.3k
views
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon cqn tximport deseq2 rnaseq
updated 7.1 years ago by 41k • written 7.1 years ago by ▴ 30
0
votes
5
replies
3.7k
views
GC content and length bias correction with DESeq2 using cqn normalization factor matrix
deseq2 cqn noiseq
updated 7.0 years ago by 41k • written 7.0 years ago by ▴ 10
1
vote
1
reply
1.2k
views
How to normalization counts matrix by GC content and sizeFactors using DESeq2 and CQN?
deseq2 cqn
updated 6.8 years ago by 41k • written 6.8 years ago by ▴ 10
4
votes
2
replies
1.2k
views
Normalize to additional variable (brain weight) in DESeq2
deseq2 cqn normalization normalized counts
updated 6.5 years ago by 41k • written 6.5 years ago by • 0
6
votes
9
replies
4.9k
views
Filtering for ATAC-seq
atac-seq CQN edger
updated 6.0 years ago by ★ 28k • written 6.0 years ago by • 0
3
votes
12
replies
1.4k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 12 months ago by 41k • written 12 months ago by ▴ 10
0
votes
1
reply
1.3k
views
CQN Package
RNASeq cqn RNASeq cqn
updated 11.8 years ago by ★ 6.5k • written 11.8 years ago by ▴ 30
0
votes
1
reply
1.1k
views
Error message running through CQN Vignette
Cancer cqn Cancer cqn
updated 11.8 years ago by ★ 6.5k • written 11.8 years ago by ★ 2.0k
0
votes
1
reply
1.3k
views
CQN normalization
cqn cqn
updated 11.7 years ago by ★ 6.5k • written 11.8 years ago by ▴ 90
0
votes
2
replies
1.8k
views
using offsets from EDASeq and cqn
GO edgeR cqn EDASeq GO edgeR cqn EDASeq
11.2 years ago love ▴ 150
0
votes
1
reply
1.5k
views
using offsets from EDASeq and cqn for edgeR
cqn EDASeq cqn EDASeq
updated 11.2 years ago by ★ 6.5k • written 11.2 years ago by 50k
0
votes
1
reply
2.5k
views
Large logCPM values when using offsets in edgeR for normalization
Sequencing edgeR cqn EDASeq Sequencing edgeR cqn EDASeq
updated 11.1 years ago by 50k • written 11.1 years ago by ▴ 90
0
votes
1
reply
737
views
error using cqn package
Normalization cqn
updated 3.4 years ago by 65k • written 3.4 years ago by ▴ 30
2
votes
6
replies
1.2k
views
DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2 cqn EDASeq
2.9 years ago Saulius • 0
1
vote
1
reply
863
views
CQN to DESeq2
cqn DESeq2
updated 20 months ago by 41k • written 21 months ago by • 0
0
votes
2
replies
766
views
cqn package : Error in if (any(lengths <= 0)) stop("argument 'lengths' need to be greater than zero") : missing value where TRUE/FALSE needed
Normalization R cqn
17 months ago Sally • 0
1
vote
3
replies
1.2k
views
Error using Conditional Quartile Normalization (CQN)
RNAseq normalization CQN conditionalquartilenormalization debugging
updated 5.1 years ago by ★ 6.5k • written 5.1 years ago by • 0
2
votes
1
reply
1.4k
views
Normalize within-/between-samples RNA-seq counts to weight networks
normalization CQN deseq2 RNA-seq network
updated 4.9 years ago by 41k • written 4.9 years ago by • 0
0
votes
1
reply
1.1k
views
Conditional Quantile Normalization (cqn) error
cqn normalization conditionalquantilenormalization atac-seq
updated 4.8 years ago by ★ 6.5k • written 4.8 years ago by • 0
0
votes
6
replies
2.1k
views
CQN to DEseq2
CQN deseq2
updated 16 months ago by • 0 • written 4.4 years ago by • 0
0
votes
1
reply
940
views
Is CQN compatible with DESeq2?
deseq2 cqn
updated 4.4 years ago by 41k • written 4.4 years ago by • 0
0
votes
0
replies
1.1k
views
What is the difference between 'sigma' and 'sig2' in CQN package?
cqn sqn
8.3 years ago s1437643 ▴ 20
0
votes
0
replies
705
views
cqn vignette error
cqn normalization edger
4.4 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
904
views
package announcement: cqn
Normalization cqn Normalization cqn
12.8 years ago Kasper Daniel Hansen ★ 6.5k
0
votes
0
replies
645
views
CQN Normalization not removing bias
cqn
4.4 years ago nicholas.macknight • 0
34 results • Page 1 of 1
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
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Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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Scholar to Robert Castelo ★ 3.2k
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