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Showing :
questions
1
vote
2
replies
864
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
2.4 years ago • updated 2.3 years ago
A
▴ 40
1
vote
3
replies
1.5k
views
Can VST be run without runing DESeq or estimateSizeFactors
DESeq2
2.6 years ago
A
▴ 40
4
votes
9
replies
1.4k
views
Variance stabilising transformation to within given range
DESeq2
scaling
vst
updated 3.2 years ago by
Wolfgang Huber
★ 13k • written 3.2 years ago by
A
▴ 40
1
vote
5
replies
996
views
technical replicates and normalization/log transformation
deseq2
normalization
updated 3.6 years ago by
Michael Love
41k • written 3.6 years ago by
A
▴ 40
1
vote
1
reply
504
views
A question for clarification regarding counts input to DESeqDataSetFromMatrix
deseq2
updated 3.9 years ago by
Michael Love
41k • written 3.9 years ago by
A
▴ 40
2
votes
2
replies
1.3k
views
subsetting VST counts from one dataset
deseq2
rna-seq
updated 4.0 years ago by
Michael Love
41k • written 4.0 years ago by
A
▴ 40
0
votes
0
replies
702
views
Error when trying to read in idat files in methylumi
methylumi
450k
methylation
methylome
4.3 years ago
A
▴ 40
0
votes
6
replies
1.9k
views
Batch effects between different sequencing runs
deseq2
batchcorrection
updated 4.6 years ago by
swbarnes2
★ 1.3k • written 4.6 years ago by
A
▴ 40
0
votes
6
replies
2.3k
views
Extracting VST matrix with batch effects removed
deseq2
batchcorrection
4.6 years ago
A
▴ 40
0
votes
2
replies
634
views
Creating a similarity matrix for genes and not values
similarity matrix
common genes
recurring groups
updated 5.2 years ago by
James W. MacDonald
65k • written 5.2 years ago by
A
▴ 40
0
votes
7
replies
1.4k
views
Results table completely wrong for specified contrast of
DESeq2
logfoldchange
counts
updated 5.3 years ago by
Michael Love
41k • written 5.3 years ago by
A
▴ 40
2
votes
1
reply
1.3k
views
Data preparation and Machine learning on time course RNAseq data
machine learning
deep learning
RNAseq
MLSeq
5.3 years ago
A
▴ 40
1
vote
5
replies
1.2k
views
Can DEXSeq ouput be used directly as an input for IsoformSwitchAnalyzeR
isoformswitchanalyzer
isoform
differential isoform usage
written 5.4 years ago by
A
▴ 40
0
votes
9
replies
2.6k
views
mapping FASTQ files to single gene (fluorescent reporter)
rsubread
alignment
align
5.4 years ago
A
▴ 40
0
votes
9
replies
2.9k
views
Featurecounts issue for counting exons: Not matching total counts mapped for specific gene
featurecounts
Rsubread
ggbio
updated 5.4 years ago by
Wei Shi
★ 3.6k • written 5.4 years ago by
A
▴ 40
0
votes
0
replies
876
views
Quantifying reporter expression to validate sequencing
alignment
Fastq
fasta
5.5 years ago
A
▴ 40
0
votes
2
replies
972
views
Preparation of summarizedExperiment for dexSeq
dexseq
genomicalignments
genomicfeatures
genomicranges
5.6 years ago
A
▴ 40
0
votes
8
replies
751
views
Duplication of same sample as if two different samples
deseq2
updated 5.6 years ago by
Michael Love
41k • written 5.6 years ago by
A
▴ 40
1
vote
4
replies
1.5k
views
venDiagram after limma showing more genes after specifying up or down regulated specifically
venn diagram
venndiagram
limma
microarray
differential expression
updated 5.8 years ago by
James W. MacDonald
65k • written 5.8 years ago by
A
▴ 40
1
vote
5
replies
1.3k
views
DEXSeq time course design
DEXSeq
differential exon usage
updated 5.9 years ago by
Alejandro Reyes
★ 1.9k • written 5.9 years ago by
A
▴ 40
1
vote
3
replies
1.0k
views
Results counts post DESeq same raw counts
DESeq2
results
updated 6.0 years ago by
Michael Love
41k • written 6.0 years ago by
A
▴ 40
0
votes
0
replies
967
views
Metadata sheet for DEXSeq analysis
dexseq
differential isoform usage
isoforms
summarizeoverlaps
granges
6.1 years ago
A
▴ 40
1
vote
2
replies
897
views
Interpretation of results names after LRT
DESeq2
LRT
multiple time points
updated 6.2 years ago by
Michael Love
41k • written 6.2 years ago by
A
▴ 40
0
votes
3
replies
1.2k
views
Error in DESeq "object" not found
deseq2
LRT
reduced model
updated 6.2 years ago by
James W. MacDonald
65k • written 6.2 years ago by
A
▴ 40
0
votes
2
replies
1.2k
views
Filtering genes with a minimum number of counts between samples
DESeq2
filtering
updated 6.2 years ago by
Michael Love
41k • written 6.2 years ago by
A
▴ 40
3
votes
8
replies
1.4k
views
Filtering for genes >100 counts after LRT still showing significant genes with genes with 0 counts!
LRT
CPM
lowcountgenes
deseq2
6.2 years ago
A
▴ 40
0
votes
4
replies
1.7k
views
Problem converting first column to rownames
deseq2
countdata
updated 6.2 years ago by
Michael Love
41k • written 6.2 years ago by
A
▴ 40
0
votes
2
replies
878
views
DESeq2, no significantly DE genes
deseq2
differential expression
adjusted pvalue
updated 6.3 years ago by
Michael Love
41k • written 6.3 years ago by
A
▴ 40
0
votes
2
replies
2.0k
views
Differential expression between multiple groups
multiple groups
differential gene expression
microarray
6.4 years ago
A
▴ 40
1
vote
2
replies
1.3k
views
Subsetting GSE data with information from two different slots
GSE
subsetting
microarray
updated 6.5 years ago by
Axel Klenk
★ 1.0k • written 6.5 years ago by
A
▴ 40
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