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DGElist
•
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0
votes
2
replies
135
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
17 days ago
prity6459
• 0
2
votes
2
replies
617
views
Inccorect group number in DGEList
edgeR
Bioconductor
Dseq2
dgelist
updated 16 months ago by
Gordon Smyth
50k • written 16 months ago by
Fiona
• 0
1
vote
1
reply
840
views
Optimal edgeR design for a single-factor experiment
factors
edgeR
setup
DGELIst
updated 3.0 years ago by
Gordon Smyth
50k • written 3.0 years ago by
Alex
• 0
0
votes
2
replies
1.7k
views
create DGElist Object
edger
DGElist
updated 5.1 years ago by
Gordon Smyth
50k • written 5.1 years ago by
naser.sadri
• 0
0
votes
4
replies
1.7k
views
Error in RnaSeqGeneEdgeRQL
dgelist
edger
RnaSeqGeneEdgeRQL
updated 5.8 years ago by
Gordon Smyth
50k • written 5.8 years ago by
Kevin
• 0
1
vote
4
replies
2.0k
views
edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
edgeR
summarizedexperiment
dgelist
6.1 years ago
aljoscha.leusmann
• 0
0
votes
0
replies
925
views
Using log2FC distance matrix in Boot.Phylo to create bootstrapped trees
tree
bootstrap
dgelist
plotmds
6.2 years ago
Larry K.
• 0
0
votes
1
reply
2.2k
views
DGEList remove/exclude rows with entrezgene = 'NA'
edger
dgelist
NA
egsea
updated 6.2 years ago by
Gordon Smyth
50k • written 6.2 years ago by
belmore
• 0
3
votes
3
replies
3.6k
views
Correct annotation of DGEList object from edgeR package regarding an RNA-Seq dataset
edger
DGEList
org.hs.eg.db
gene annotation
updated 2.6 years ago by
IIart.hubII
• 0 • written 6.4 years ago by
svlachavas
▴ 830
0
votes
2
replies
3.0k
views
Design of 'group' object in DGElist function
egder
dgelist
group
rnaseq
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
fawazfebin
▴ 60
2
votes
4
replies
3.2k
views
Filtering DGEList object in edgeR
DGElist
filter
edgeR
updated 6.8 years ago by
Gordon Smyth
50k • written 6.8 years ago by
alakatos
▴ 130
3
votes
6
replies
2.5k
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 7.7 years ago by
Steve Lianoglou
★ 13k • written 7.7 years ago by
benedict.ng
▴ 20
3
votes
7
replies
6.6k
views
edgeR subsetting DGEList by column/sample
edger
subsetting
dgelist
updated 7.8 years ago by
Gordon Smyth
50k • written 7.8 years ago by
mnaymik
▴ 10
1
vote
4
replies
20k
views
edgeR: non-unique values when setting 'row.names' - but the row names are unique!!!
edgeR
row.names
DGEList
9.3 years ago • updated 9.2 years ago
ccheung
• 0
14 results • Page
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Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I looked into the genomic distributions. Please see the screenshot attatched ![ distrubution for female loci, boot1 and boot2][1] how do …
Answer: How to save the DEXSeq results
by
Michael Love
41k
If you look at the output here: https://bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.html#4_Testing_for_differe…
Answer: Method to find pathways different between 2 groups
by
Robert Castelo
★ 3.3k
Hi, regarding how could you combine the result from each tool, one option is using a so-called "ensembl method", for instance, the package …
Answer: Couldn't connect to server while using "pathways"
by
James W. MacDonald
65k
As ATpoint already noted, you should proceed from the assumption that your audience knows nothing about what you are doing, and provide eno…
Answer: Trim/Filter out-of-bounds GRanges
by
Michael Love
41k
https://support.bioconductor.org/p/73432/#73448
Votes
Answer: Method to find pathways different between 2 groups
Answer: Method to find pathways different between 2 groups
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Method to find pathways different between 2 groups
Comment: Trying to use enrichGO
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