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pheatmap
•
reset
4
votes
8
replies
7.9k
views
Scaling genes to have unit variance for clustering / heatmaps with DESeq2
deseq2
heatmap.2
bicluster
pheatmap
updated 6.5 years ago by
Michael Love
41k • written 8.7 years ago by
tj.hu
▴ 10
0
votes
6
replies
1.5k
views
stringasfactor = F changes the output of pheatmap, why?
deseq2
pheatmap
updated 5.2 years ago by
Wolfgang Huber
★ 13k • written 5.2 years ago by
bdy8
▴ 10
4
votes
5
replies
4.0k
views
Deseq2 unsupervised analysis (heatmap row scaling or none?)
deseq2
pheatmap
8.2 years ago
jarod_v6@libero.it
▴ 40
0
votes
2
replies
1.7k
views
Unsupervised analysis problems
pheatmap
unsupervised
updated 8.2 years ago by
Michael Love
41k • written 8.2 years ago by
jarod_v6@libero.it
▴ 40
1
vote
2
replies
2.5k
views
R crash when matrix nrows exceeds 45000 using pheatmap/heatmap.2
pheatmap
heatmap.2
8.1 years ago
John
▴ 30
5
votes
11
replies
2.6k
views
Heatmap only including DE genes?
heatmap
coolmap
pheatmap
updated 4.0 years ago by
Gordon Smyth
50k • written 4.0 years ago by
Raito92
▴ 60
0
votes
2
replies
550
views
Heat Map
ColData
pheatmap
DESeq2
written 10 months ago by
dania.khalid
• 0
2
votes
4
replies
1.8k
views
Issues with Pheatmap
pheatmap
2.1 years ago
axe880
• 0
0
votes
4
replies
4.9k
views
Pheatmap/Complexheatmap: making a continuous color scale with NAs
R
Pathways
pheatmap
limma
updated 3.1 years ago by
SamGG
▴ 350 • written 3.1 years ago by
r.i.s.alnuwaysir
▴ 10
0
votes
4
replies
15k
views
hclust(d, method = method) : NA/NaN/Inf in foreign function call (arg 10)
R
pheatmap
xcms
updated 20 months ago by
James W. MacDonald
65k • written 2.7 years ago by
onokaisaac
• 0
2
votes
1
reply
2.2k
views
deseq 2x2: highly variable genes are not among differentially expressed gene
deseq2
rld
pheatmap
dds
updated 6.5 years ago by
Michael Love
41k • written 8.6 years ago by
rahel14350
▴ 10
0
votes
2
replies
3.8k
views
Scaling for p.heatmap
heatmaps
pheatmap
scaling
22 months ago
Bhavana
• 0
0
votes
1
reply
241
views
Changed DESeq2 comparison value but the heatmap is still the same
DESeq2
pheatmap
updated 8 weeks ago by
James W. MacDonald
65k • written 8 weeks ago by
zhangaimei
• 0
1
vote
1
reply
5.4k
views
adding margins around pheatmap plots
pheatmap
updated 7.7 years ago by
Wolfgang Huber
★ 13k • written 7.7 years ago by
stephane.plaisance
▴ 10
8
votes
1
reply
9.2k
views
extracting the genes associated with the clusters
heatmap.2
pheatmap
complexheatmap
heatplus
updated 7.2 years ago by
Gavin Kelly
▴ 680 • written 7.2 years ago by
Bogdan
▴ 670
0
votes
1
reply
1.0k
views
How to solve out the misunstanding of fake "red" "green" on the heatmap
pheatmap
updated 7.0 years ago by
Gavin Kelly
▴ 680 • written 7.0 years ago by
joseph
▴ 50
0
votes
1
reply
2.7k
views
How to extract the distrances of the column dendrogram from pheatmap and just plot them with the distance scale?
pheatmap
hclust
R
dendrogram
7.0 years ago
vd4mmind
• 0
0
votes
1
reply
2.1k
views
Unsupervised heatmap use tpm or rlog gave different results
deseq2
tpm
heatmap
pheatmap
updated 6.9 years ago by
Michael Love
41k • written 6.9 years ago by
jarod_v6@libero.it
▴ 40
0
votes
2
replies
1.5k
views
Averaging over biological replicates with DESeq2 for heatmap plotting
deseq2
pheatmap
average
updated 5.6 years ago by
James W. MacDonald
65k • written 5.6 years ago by
chighfi
• 0
0
votes
4
replies
2.8k
views
Error when loading MSnbase package "object 'vI' not found"
msnbase
xcms
pheatmap
5.1 years ago
lmg
• 0
0
votes
1
reply
4.7k
views
Reordering clusters when plotting pheatmap in R
R
pheatmap
clusters
4.8 years ago
ecg1g15
▴ 20
0
votes
1
reply
2.4k
views
Annotation in pheatmap
pheatmap
updated 21 months ago by
Guido Hooiveld
★ 3.9k • written 21 months ago by
Rob
• 0
2
votes
4
replies
8.7k
views
pheatmap for DEGs
normalization
pheatmap
updated 4.0 years ago by
Kevin Blighe
★ 3.9k • written 4.0 years ago by
Hamidreza Hashemi
▴ 20
0
votes
2
replies
5.0k
views
plotPCA with DESeq2 results in unable to find an inherited method for function plotPCA for signature matrix Error
deseq2
pheatmap
RColorBrewer
BiocGenerics
updated 3.9 years ago by
Michael Love
41k • written 3.9 years ago by
matthewzli777
• 0
0
votes
2
replies
7.8k
views
Add selected row names on pheatmap
R
pheatmap
updated 3.4 years ago by
ATpoint
★ 4.1k • written 3.4 years ago by
ecg1g15
▴ 20
0
votes
1
reply
971
views
Plotting the most expressed genes after conducting DESeq2
DESeq2
pheatmap
apeglm
updated 3.2 years ago by
Michael Love
41k • written 3.2 years ago by
amoaristotle
▴ 10
0
votes
1
reply
2.4k
views
Can you colour dendrogram branch clusters in pheatmap?
R
heatmaps
pheatmap
updated 3.2 years ago by
Kevin Blighe
★ 3.9k • written 3.2 years ago by
trichorico
▴ 10
0
votes
0
replies
6.5k
views
Pheatmap: how to use breaks for pheatmap
pheatmap
heatmap
7.5 years ago
jarod_v6@libero.it
▴ 40
0
votes
0
replies
2.7k
views
pheatmap - Error in do_one(nmeth) : NA/NaN/Inf in foreign function call (arg 1)
pheatmap
kmeans
6.5 years ago
Assa Yeroslaviz
★ 1.5k
4
votes
9
replies
7.8k
views
Upper triangular matrix heatmap using pheatmap package
pheatmap
8.4 years ago
Deepak Tanwar
▴ 10
1
vote
0
replies
2.6k
views
heatmap.2() making columns narrower to make them look like microarray?
heatmap.2
pheatmap
8.6 years ago
AJC
▴ 10
1
vote
3
replies
9.9k
views
Sorting columns in pheatmap
pheatmap
updated 3.0 years ago by
Chris Seidel
▴ 80 • written 3.0 years ago by
Linda
• 0
1
vote
1
reply
11k
views
Pheatmap clustering and row annotation
R
pheatmap
cutree
6.6 years ago
meseretbrihanu
▴ 10
33 results • Page
1 of 1
Recent ...
Replies
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Comment: Store output of matchPWM()
by
James W. MacDonald
65k
Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…
Votes
Answer: DEseq2 coefficient
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
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