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DGELIst
•
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0
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2
replies
429
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
9 months ago
prity6459
• 0
2
votes
2
replies
811
views
Inccorect group number in DGEList
edgeR
Bioconductor
Dseq2
dgelist
updated 2.1 years ago by
Gordon Smyth
52k • written 2.1 years ago by
Fiona
• 0
1
vote
1
reply
1.1k
views
Optimal edgeR design for a single-factor experiment
factors
edgeR
setup
DGELIst
updated 3.7 years ago by
Gordon Smyth
52k • written 3.7 years ago by
Alex
• 0
0
votes
2
replies
2.1k
views
create DGElist Object
edger
DGElist
updated 5.8 years ago by
Gordon Smyth
52k • written 5.8 years ago by
naser.sadri
• 0
0
votes
4
replies
2.0k
views
Error in RnaSeqGeneEdgeRQL
dgelist
edger
RnaSeqGeneEdgeRQL
updated 6.5 years ago by
Gordon Smyth
52k • written 6.5 years ago by
Kevin
• 0
1
vote
4
replies
2.5k
views
edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
edgeR
summarizedexperiment
dgelist
6.8 years ago
aljoscha.leusmann
• 0
0
votes
0
replies
1.1k
views
Using log2FC distance matrix in Boot.Phylo to create bootstrapped trees
tree
bootstrap
dgelist
plotmds
6.9 years ago
Larry K.
• 0
0
votes
1
reply
2.5k
views
DGEList remove/exclude rows with entrezgene = 'NA'
edger
dgelist
NA
egsea
updated 6.9 years ago by
Gordon Smyth
52k • written 6.9 years ago by
belmore
• 0
3
votes
3
replies
4.1k
views
Correct annotation of DGEList object from edgeR package regarding an RNA-Seq dataset
edger
DGEList
org.hs.eg.db
gene annotation
updated 3.3 years ago by
IIart.hubII
• 0 • written 7.2 years ago by
svlachavas
▴ 840
0
votes
2
replies
3.5k
views
Design of 'group' object in DGElist function
egder
dgelist
group
rnaseq
updated 7.2 years ago by
Aaron Lun
★ 28k • written 7.2 years ago by
fawazfebin
▴ 60
2
votes
4
replies
3.7k
views
Filtering DGEList object in edgeR
DGElist
filter
edgeR
updated 7.6 years ago by
Gordon Smyth
52k • written 7.6 years ago by
alakatos
▴ 130
4
votes
6
replies
2.9k
views
How to carry out differential gene expression starting with a table of TMM normalised values without access to the raw reads?
edger
raw reads
TMM normalised values
DGEList
differential gene expression
updated 8.5 years ago by
Steve Lianoglou
★ 13k • written 8.5 years ago by
benedict.ng
▴ 30
3
votes
7
replies
7.2k
views
edgeR subsetting DGEList by column/sample
edger
subsetting
dgelist
updated 8.5 years ago by
Gordon Smyth
52k • written 8.5 years ago by
mnaymik
▴ 10
1
vote
4
replies
21k
views
edgeR: non-unique values when setting 'row.names' - but the row names are unique!!!
edgeR
row.names
DGEList
10.0 years ago
ccheung
• 0
14 results • Page
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Replies
Comment: input for singR function
by
iamin053
• 0
Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!
Comment: build samplesheet and plot profile
by
yf
• 0
![enter image description here][1] [1]: /media/images/8ea93bd0-bc90-443d-a332-4701f54a
Answer: I am having issues with bowtie2_build
by
James W. MacDonald
67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues
by
Michael Love
43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview
by
Guido Hooiveld
★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Votes
A: Doubt about the "zero expression" genes or genes with no reads at all in the co
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Selection of correct coefficients or contrasts in DESeq2
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