Showing : CQN • reset
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
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 10.1 years ago by 25k • written 10.1 years ago by ▴ 350
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
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 7.2 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
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
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
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
0
votes
6
replies
2.1k
views
CQN to DEseq2
CQN deseq2
updated 17 months ago by • 0 • written 4.4 years ago by • 0
0
votes
9
replies
2.1k
views
DESeq2 stuck running
cqn DESeq2 cqn DESeq2
updated 10.0 years ago by 41k • written 10.0 years ago by ★ 13k
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
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
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
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
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
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
1.3k
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
1.3k
views
CQN normalization
cqn cqn
updated 11.7 years ago by ★ 6.5k • written 11.8 years ago by ▴ 90
2
votes
2
replies
1.3k
views
CQN and EdgeR Library Size for Normalization
CQN atac-seq normalization edgeR
6.0 years ago shankasal • 0
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
2
votes
6
replies
1.2k
views
DESeq2, why are the signs of EDASeq offsets flipped compared to CQN ?
DESeq2 cqn EDASeq
3.0 years ago Saulius • 0
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
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
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
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
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
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
904
views
package announcement: cqn
Normalization cqn Normalization cqn
12.8 years ago Kasper Daniel Hansen ★ 6.5k
1
vote
1
reply
864
views
CQN to DESeq2
cqn DESeq2
updated 21 months ago by 41k • written 21 months ago by • 0
0
votes
2
replies
770
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
0
votes
1
reply
738
views
error using cqn package
Normalization cqn
updated 3.4 years ago by 65k • written 3.4 years ago by ▴ 30
0
votes
0
replies
708
views
cqn vignette error
cqn normalization edger
4.4 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
648
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: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough?
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
This comment helps.
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
I am not sure how your comment helps here?
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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