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How to increase font for gene name and increase arrow size for GVIZ's ( UcscTrack function ) track?
DMRcate Gviz
updated 5 weeks ago by • 0 • written 3.2 years ago by ▴ 50
4
votes
2
replies
614
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Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 11 weeks ago by 52k • written 11 weeks ago by ▴ 50
3
votes
3
replies
644
views
Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 6 months ago by 68k • written 6 months ago by ▴ 50
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0
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2.4k
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Comment: Comment: Help with limma contrast, difference of a difference?
2.6 years ago Ahdee ▴ 50
0
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0
replies
2.4k
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Comment: Comment: Help with limma contrast, difference of a difference?
2.6 years ago Ahdee ▴ 50
0
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1
reply
2.4k
views
Comment: Comment: Help with limma contrast, difference of a difference?
2.6 years ago Ahdee ▴ 50
3
votes
9
replies
2.4k
views
Help with limma contrast, difference of a difference?
limma
2.6 years ago Ahdee ▴ 50
0
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1
reply
2.4k
views
Comment: Comment: Help with limma contrast, difference of a difference?
2.6 years ago Ahdee ▴ 50
2
votes
1
reply
801
views
Is it possible to speed up VariantAnnotation's rowRanges function when converting to a dataframe?
varian VariantToolsData
updated 2.7 years ago by 68k • written 2.7 years ago by ▴ 50
0
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1
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1.3k
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Comment: Comment: Need help with a contrast design for limma with a missing group?
3.0 years ago Ahdee ▴ 50
0
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3
replies
1.3k
views
Need help with a contrast design for limma with a missing group?
limma VOOM
updated 3.0 years ago by 52k • written 3.0 years ago by ▴ 50
0
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0
replies
908
views
Is it possible to output ensembl id for annotatr build_annotations basicgenes?
Annotation annotatr
3.2 years ago Ahdee ▴ 50
0
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0
replies
1.7k
views
Comment: Comment: Confused about using ComBat_seq with voom and limma? Should run batch as a cova
3.5 years ago Ahdee ▴ 50
0
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0
replies
3.8k
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Comment: Comment: How to count barcode sequences in a fastq file
3.5 years ago Ahdee ▴ 50
1
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2
replies
1.7k
views
Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva limma
3.5 years ago Ahdee ▴ 50
0
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0
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2.5k
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Comment: Comment: How to filter EnsDb into another EnsDb object instead of GRange?
3.7 years ago Ahdee ▴ 50
0
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1
reply
2.5k
views
Comment: Comment: How to filter EnsDb into another EnsDb object instead of GRange?
3.7 years ago Ahdee ▴ 50
0
votes
1
reply
2.5k
views
Comment: Comment: How to filter EnsDb into another EnsDb object instead of GRange?
3.7 years ago Ahdee ▴ 50
1
vote
9
replies
2.5k
views
How to filter EnsDb into another EnsDb object instead of GRange?
ens ensembldb EnsDb.Hsapiens.v86 EnsDb.Rnorvegicus.v75
3.7 years ago Ahdee ▴ 50
0
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0
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2.5k
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Comment: Comment: How to filter EnsDb into another EnsDb object instead of GRange?
3.7 years ago Ahdee ▴ 50
0
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1
reply
2.5k
views
Comment: Comment: How to calculate coefficient of variation within group?
3.9 years ago Ahdee ▴ 50
0
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3
replies
2.5k
views
How to calculate coefficient of variation within group?
edgeR limma RNASeqPower
updated 3.0 years ago by 52k • written 3.9 years ago by ▴ 50
0
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0
replies
965
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Comment: C: In EdgeR TMM and/or voom is it better to normalize all samples, even if some wil
4.5 years ago Ahdee ▴ 50
2
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2
replies
965
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In EdgeR TMM and/or voom is it better to normalize all samples, even if some will not be used for comparisons?
edger limma
updated 4.5 years ago by 52k • written 4.5 years ago by ▴ 50
0
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1
reply
2.7k
views
Comment: C: tximport from RSEM expected counts: is it possible to import from a table rather
4.5 years ago Ahdee ▴ 50
1
vote
7
replies
2.7k
views
tximport from RSEM expected counts: is it possible to import from a table rather than a file?
tximport limma rnaseq
updated 3.9 years ago by • 0 • written 4.7 years ago by ▴ 50
0
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0
replies
908
views
Answer: A: Custom pathway for limma's kegga?
4.8 years ago Ahdee ▴ 50
0
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1
reply
908
views
Custom pathway for limma's kegga?
limma
4.8 years ago Ahdee ▴ 50
0
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0
replies
1.9k
views
Comment: C: Can I use (length bias normalization) from packages like EDAseq or cqn for input
5.1 years ago Ahdee ▴ 50
0
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0
replies
1.9k
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Comment: C: Can I use (length bias normalization) from packages like EDAseq or cqn for input
5.1 years ago Ahdee ▴ 50
0
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1
reply
1.9k
views
Comment: C: Can I use (length bias normalization) from packages like EDAseq or cqn for input
5.1 years ago Ahdee ▴ 50
0
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1
reply
1.9k
views
Comment: C: Can I use (length bias normalization) from packages like EDAseq or cqn for input
5.1 years ago Ahdee ▴ 50
4
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7
replies
1.9k
views
Can I use (length bias normalization) from packages like EDAseq or cqn for input into VOOM?
limma voom edaseq edger rnaseq
updated 5.1 years ago by 52k • written 5.1 years ago by ▴ 50
0
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1
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1.4k
views
Comment: C: UnProducible error with goana and kegga function
5.4 years ago Ahdee ▴ 50
0
votes
3
replies
1.4k
views
UnProducible error with goana and kegga function
limma goana kegga
updated 5.4 years ago by 52k • written 5.4 years ago by ▴ 50
0
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0
replies
1.3k
views
Comment: C: How to create two columns for model matrix used in limma?
5.4 years ago Ahdee ▴ 50
2
votes
2
replies
1.3k
views
How to create two columns for model matrix used in limma?
limma edger
updated 5.5 years ago by 52k • written 5.5 years ago by ▴ 50
0
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1
reply
891
views
Comment: C: Limma model design: is it better to just build a separate design for each specif
5.7 years ago Ahdee ▴ 50
0
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1
reply
891
views
Comment: C: Limma model design: is it better to just build a separate design for each specif
5.7 years ago Ahdee ▴ 50
4
votes
6
replies
891
views
Limma model design: is it better to just build a separate design for each specific comparison?
limma
updated 5.7 years ago by 68k • written 5.7 years ago by ▴ 50
0
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0
replies
1.3k
views
Comment: C: Why does limma voom E value give different result than the voom object
5.7 years ago Ahdee ▴ 50
0
votes
0
replies
13k
views
Comment: C: Seurat 2.3.4 installation
5.7 years ago Ahdee ▴ 50
1
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2
replies
1.3k
views
Why does limma voom E value give different result than the voom object
limma voom rna-seq
updated 5.7 years ago by ▴ 160 • written 5.7 years ago by ▴ 50
0
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1
reply
1.0k
views
Is there a package to convert DNA coordinates to Cytogenetic location?
annotation coordinates cytogenetic
5.9 years ago Ahdee ▴ 50
0
votes
0
replies
955
views
Help with mapping Kegg hsa01100 using pathview
kegg pathway pathview
5.9 years ago Ahdee ▴ 50
4
votes
1
reply
3.1k
views
benefits of pearson distance for hierarchical clustering
heatmap.3 heatmap
updated 6.2 years ago by 68k • written 6.2 years ago by ▴ 50
0
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0
replies
2.5k
views
Comment: C: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
6.5 years ago Ahdee ▴ 50
4
votes
2
replies
2.5k
views
Where to download expected counts instead of normalized RSEM for TCGA LUAD?
limma tcga
updated 6.5 years ago by ★ 13k • written 6.5 years ago by ▴ 50
0
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0
replies
1.0k
views
Comment: C: Combining groups in a LIMMA design
6.5 years ago Ahdee ▴ 50
3
votes
2
replies
1.0k
views
Combining groups in a LIMMA design
limma
6.5 years ago Ahdee ▴ 50
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