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3
votes
3
replies
442
views
Optimizing CPM Calculation for Varied RNA-seq Data
edgeR
updated 7 weeks ago by 67k • written 7 weeks ago by ▴ 50
0
votes
0
replies
2.2k
views
Comment: Comment: Help with limma contrast, difference of a difference?
2.3 years ago Ahdee ▴ 50
0
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0
replies
2.2k
views
Comment: Comment: Help with limma contrast, difference of a difference?
2.3 years ago Ahdee ▴ 50
0
votes
1
reply
2.2k
views
Comment: Comment: Help with limma contrast, difference of a difference?
2.3 years ago Ahdee ▴ 50
3
votes
9
replies
2.2k
views
Help with limma contrast, difference of a difference?
limma
2.3 years ago Ahdee ▴ 50
0
votes
1
reply
2.2k
views
Comment: Comment: Help with limma contrast, difference of a difference?
2.3 years ago Ahdee ▴ 50
2
votes
1
reply
694
views
Is it possible to speed up VariantAnnotation's rowRanges function when converting to a dataframe?
varian VariantToolsData
updated 2.3 years ago by 67k • written 2.3 years ago by ▴ 50
0
votes
1
reply
1.2k
views
Comment: Comment: Need help with a contrast design for limma with a missing group?
2.6 years ago Ahdee ▴ 50
0
votes
3
replies
1.2k
views
Need help with a contrast design for limma with a missing group?
limma VOOM
updated 2.6 years ago by 51k • written 2.6 years ago by ▴ 50
0
votes
0
replies
823
views
Is it possible to output ensembl id for annotatr build_annotations basicgenes?
Annotation annotatr
2.8 years ago Ahdee ▴ 50
0
votes
0
replies
1.1k
views
How to increase font for gene name and increase arrow size for GVIZ's ( UcscTrack function ) track?
DMRcate Gviz
2.8 years ago Ahdee ▴ 50
0
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0
replies
1.6k
views
Comment: Comment: Confused about using ComBat_seq with voom and limma? Should run batch as a cova
3.1 years ago Ahdee ▴ 50
0
votes
0
replies
3.6k
views
Comment: Comment: How to count barcode sequences in a fastq file
3.1 years ago Ahdee ▴ 50
1
vote
2
replies
1.6k
views
Confused about using ComBat_seq with voom and limma? Should run batch as a covariate and use uncorrected instead?
sva limma
3.1 years ago Ahdee ▴ 50
0
votes
0
replies
2.3k
views
Comment: Comment: How to filter EnsDb into another EnsDb object instead of GRange?
3.3 years ago Ahdee ▴ 50
0
votes
1
reply
2.3k
views
Comment: Comment: How to filter EnsDb into another EnsDb object instead of GRange?
3.3 years ago Ahdee ▴ 50
0
votes
1
reply
2.3k
views
Comment: Comment: How to filter EnsDb into another EnsDb object instead of GRange?
3.3 years ago Ahdee ▴ 50
1
vote
9
replies
2.3k
views
How to filter EnsDb into another EnsDb object instead of GRange?
ens ensembldb EnsDb.Hsapiens.v86 EnsDb.Rnorvegicus.v75
3.3 years ago Ahdee ▴ 50
0
votes
0
replies
2.3k
views
Comment: Comment: How to filter EnsDb into another EnsDb object instead of GRange?
3.3 years ago Ahdee ▴ 50
0
votes
1
reply
2.2k
views
Comment: Comment: How to calculate coefficient of variation within group?
3.6 years ago Ahdee ▴ 50
0
votes
3
replies
2.2k
views
How to calculate coefficient of variation within group?
edgeR limma RNASeqPower
updated 2.6 years ago by 51k • written 3.6 years ago by ▴ 50
0
votes
0
replies
867
views
Comment: C: In EdgeR TMM and/or voom is it better to normalize all samples, even if some wil
4.2 years ago Ahdee ▴ 50
2
votes
2
replies
867
views
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 4.2 years ago by 51k • written 4.2 years ago by ▴ 50
0
votes
1
reply
2.4k
views
Comment: C: tximport from RSEM expected counts: is it possible to import from a table rather
4.2 years ago Ahdee ▴ 50
1
vote
7
replies
2.4k
views
tximport from RSEM expected counts: is it possible to import from a table rather than a file?
tximport limma rnaseq
updated 3.5 years ago by • 0 • written 4.4 years ago by ▴ 50
0
votes
1
reply
807
views
Custom pathway for limma's kegga?
limma
4.5 years ago Ahdee ▴ 50
0
votes
0
replies
807
views
Answer: A: Custom pathway for limma's kegga?
4.5 years ago Ahdee ▴ 50
0
votes
0
replies
1.7k
views
Comment: C: Can I use (length bias normalization) from packages like EDAseq or cqn for input
4.8 years ago Ahdee ▴ 50
0
votes
0
replies
1.7k
views
Comment: C: Can I use (length bias normalization) from packages like EDAseq or cqn for input
4.8 years ago Ahdee ▴ 50
0
votes
1
reply
1.7k
views
Comment: C: Can I use (length bias normalization) from packages like EDAseq or cqn for input
4.8 years ago Ahdee ▴ 50
0
votes
1
reply
1.7k
views
Comment: C: Can I use (length bias normalization) from packages like EDAseq or cqn for input
4.8 years ago Ahdee ▴ 50
4
votes
7
replies
1.7k
views
Can I use (length bias normalization) from packages like EDAseq or cqn for input into VOOM?
limma voom edaseq edger rnaseq
updated 4.8 years ago by 51k • written 4.8 years ago by ▴ 50
0
votes
1
reply
1.3k
views
Comment: C: UnProducible error with goana and kegga function
5.0 years ago Ahdee ▴ 50
0
votes
3
replies
1.3k
views
UnProducible error with goana and kegga function
limma goana kegga
updated 5.0 years ago by 51k • written 5.0 years ago by ▴ 50
0
votes
0
replies
1.1k
views
Comment: C: How to create two columns for model matrix used in limma?
5.1 years ago Ahdee ▴ 50
2
votes
2
replies
1.1k
views
How to create two columns for model matrix used in limma?
limma edger
updated 5.1 years ago by 51k • written 5.1 years ago by ▴ 50
0
votes
1
reply
807
views
Comment: C: Limma model design: is it better to just build a separate design for each specif
5.3 years ago Ahdee ▴ 50
0
votes
1
reply
807
views
Comment: C: Limma model design: is it better to just build a separate design for each specif
5.3 years ago Ahdee ▴ 50
4
votes
6
replies
807
views
Limma model design: is it better to just build a separate design for each specific comparison?
limma
updated 5.3 years ago by 67k • written 5.3 years ago by ▴ 50
0
votes
0
replies
1.2k
views
Comment: C: Why does limma voom E value give different result than the voom object
5.4 years ago Ahdee ▴ 50
0
votes
0
replies
12k
views
Comment: C: Seurat 2.3.4 installation
5.4 years ago Ahdee ▴ 50
1
vote
2
replies
1.2k
views
Why does limma voom E value give different result than the voom object
limma voom rna-seq
updated 5.4 years ago by ▴ 160 • written 5.4 years ago by ▴ 50
0
votes
1
reply
921
views
Is there a package to convert DNA coordinates to Cytogenetic location?
annotation coordinates cytogenetic
5.5 years ago Ahdee ▴ 50
0
votes
0
replies
879
views
Help with mapping Kegg hsa01100 using pathview
kegg pathway pathview
5.6 years ago Ahdee ▴ 50
4
votes
1
reply
2.8k
views
benefits of pearson distance for hierarchical clustering
heatmap.3 heatmap
updated 5.8 years ago by 67k • written 5.8 years ago by ▴ 50
0
votes
0
replies
2.3k
views
Comment: C: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
6.1 years ago Ahdee ▴ 50
4
votes
2
replies
2.3k
views
Where to download expected counts instead of normalized RSEM for TCGA LUAD?
limma tcga
updated 6.1 years ago by ★ 13k • written 6.1 years ago by ▴ 50
0
votes
0
replies
952
views
Comment: C: Combining groups in a LIMMA design
6.2 years ago Ahdee ▴ 50
3
votes
2
replies
952
views
Combining groups in a LIMMA design
limma
6.2 years ago Ahdee ▴ 50
0
votes
0
replies
809
views
Comment: C: Run edgeR or Voom+LIMMA where groups are dynamically reassigned for each gene.
6.2 years ago Ahdee ▴ 50
73 results • Page 1 of 2
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