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smallrna
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2
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10
replies
2.1k
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DEseq normalization Small RNA-seq data using rRNA
deseq2
normalization
smallrna
ribosomal rna
7.5 years ago
mosharrofgeb
▴ 10
0
votes
1
reply
2.0k
views
DESeq with no replicates
Sequencing
miRNA
SmallRNA
DESeq
Sequencing
miRNA
SmallRNA
DESeq
updated 13.4 years ago by
Wolfgang Huber
★ 13k • written 13.4 years ago by
Wu, Xiwei
▴ 350
0
votes
1
reply
1.9k
views
Is normalization in edgeR required for small RNA sequencing data?
Sequencing
SmallRNA
edgeR
Sequencing
SmallRNA
edgeR
updated 11.6 years ago by
Mark Robinson
▴ 880 • written 11.6 years ago by
Danie
▴ 40
6
votes
7
replies
1.9k
views
Normalization for small non-coding RNA
TMM
deseq2
smallrna
rnaseq
updated 5.4 years ago by
António Miguel de Jesus Domingues
▴ 490 • written 5.4 years ago by
Konstantinos Yeles
▴ 80
0
votes
1
reply
1.8k
views
Bioconductor Digest, Vol 115, Issue 22
Transcription
Sequencing
miRNA
SmallRNA
Annotation
Normalization
GO
Cancer
Organism
edgeR
updated 11.6 years ago by
Steve Lianoglou
★ 13k • written 11.6 years ago by
Weng Khong LIM
▴ 10
0
votes
3
replies
1.6k
views
finding differential expression pattern between paired columns of data frame.
Sequencing
SmallRNA
Microarray
limma
Sequencing
SmallRNA
Microarray
limma
updated 9.7 years ago by
James W. MacDonald
65k • written 9.7 years ago by
Jakub Stanislaw Nowak
▴ 70
3
votes
7
replies
1.4k
views
small dimensions in the matrix of counts from smallRNA using DESEq2
matrix
DESeq2
SmallRNA
dimensions
small
2.6 years ago
andreia
▴ 10
2
votes
0
replies
1.2k
views
Job:
PhD Studentship - Investigating Regulation of Transcription and Translation in Prostate Cancer
mirna
riboseq
smallrna
differential gene expression
Job
6.1 years ago
Andy Lynch
▴ 120
0
votes
2
replies
1.2k
views
small RNAs quantification
smallrna
counts
7.6 years ago
ribioinfo
▴ 100
0
votes
0
replies
1.1k
views
Job:
Post-doc in Prostate Cancer Research (Statistics / Computational Biology) at University of St Andrews (+PhD position also available)
cancer
sequencing
rnaseq
methylation
smallrna
Job
5.8 years ago
Andy Lynch
▴ 120
0
votes
1
reply
915
views
small RNA counts
counts
SmallRNA
Normalization
updated 2.4 years ago by
hauken_heyken
▴ 80 • written 2.5 years ago by
k___
▴ 30
2
votes
2
replies
684
views
Contradictory results in smallRNA differential expression analysis using DESeq2
SmallRNA
DESeq2
21 months ago • updated 20 months ago
jucosie
• 0
0
votes
13
replies
655
views
Unexpected behavior of lfcShrink() function in DESeq2 analysis
DESeq2
SmallRNA
updated 8 weeks ago by
Michael Love
41k • written 8 weeks ago by
r.r.bioinf
• 0
13 results • Page
1 of 1
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Replies
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error
by
Fara
• 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
James W. MacDonald
65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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