0
votes
0
replies
1.5k
views
Problem with "TxDb.Mmusculus.UCSC.mm39.refGene" to annotate genes with ChIPseeker
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3.6 years ago Palmira • 0
0
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2
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6.3k
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What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
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3.6 years ago Bhavana • 0
0
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1
reply
1.2k
views
What are the data values in qRT-PCR for statistical testing? dCT? or 2^-dCT?
qRT-PCR CTvalue
updated 3.6 years ago by 68k • written 3.6 years ago by ▴ 10
0
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1
reply
1.9k
views
Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq DESeq2
updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
9
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9
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4.7k
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Using Age or other numerical variable to model expression in deseq2
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updated 3.6 years ago by 68k • written 3.6 years ago by • 0
0
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1
reply
1.6k
views
Bioconducter can not be installed on latest RStudio
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updated 3.6 years ago by ★ 6.6k • written 3.6 years ago by • 0
0
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1
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1.6k
views
Using queryMany() in mygene package: Problem of querying Entrez gene IDs based on UniGene IDs in rat.
mygene queryMany
updated 3.6 years ago by ★ 4.1k • written 3.6 years ago by • 0
0
votes
1
reply
1.7k
views
GC content
EDASeq
updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
0
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0
replies
824
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Timeout error when querying DGIDB
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3.6 years ago Jannah • 0
0
votes
4
replies
1.8k
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I got error message about DESeqDataSetFromMatrix
DESeq2
updated 3.6 years ago by ★ 1.4k • written 3.6 years ago by • 0
2
votes
6
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2.1k
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DESeq2: relevel() unsuccessfully setting control group
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updated 3.6 years ago by • 0 • written 4.9 years ago by ▴ 30
1
vote
3
replies
3.3k
views
miRNA differential expression analysis - treat as transcript level?
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updated 3.6 years ago by 43k • written 3.6 years ago by • 0
0
votes
0
replies
1.2k
views
Differential expression with single cell data: any good two component (hurdle) models recently?
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3.6 years ago Nik Tuzov ▴ 90
3
votes
9
replies
3.1k
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Help with limma contrast, difference of a difference?
limma
3.6 years ago Ahdee ▴ 60
0
votes
6
replies
3.8k
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How to change all text, including point labels to Arial?
EnhancedVolcano
updated 3.6 years ago by 68k • written 3.6 years ago by • 0
0
votes
1
reply
1.6k
views
DiffBind: GreyListChIP error: Error: $ operator is invalid for atomic vectors
DiffBind
updated 3.6 years ago by ★ 5.2k • written 3.6 years ago by ▴ 10
0
votes
2
replies
8.9k
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Scaling for p.heatmap
heatmaps pheatmap scaling
3.6 years ago Bhavana • 0
0
votes
4
replies
3.9k
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Confused about using RUVg in getting negative control genes using RUVg
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3.6 years ago Mohamed ▴ 30
0
votes
3
replies
2.6k
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I got error when visualizing my PCA
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updated 3.6 years ago by ▴ 180 • written 3.6 years ago by • 0
0
votes
0
replies
766
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Is there a Bioconductor package to calculate TFs regulatory networks?
TFs Transcription regulator
3.6 years ago OliverBoynton • 0
1
vote
3
replies
3.4k
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Trouble importing my own Gene Ontology Annotation into topGO
Annotation GeneOntology topGO GO
updated 3.6 years ago by 68k • written 3.6 years ago by ▴ 60
2
votes
8
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2.7k
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RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
3.6 years ago Kelen ▴ 10
0
votes
0
replies
879
views
Typo in citation for RNASeqPower
RNASeqPower citation
3.6 years ago stephenjjohnson • 0
0
votes
0
replies
644
views
diffbind dba.report
diffbind
3.6 years ago jonathanho1989 • 0
0
votes
8
replies
2.3k
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Finding differentially expressed genes in a prospective cohort study
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3.6 years ago YC • 0
1
vote
4
replies
2.1k
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How to create an aldex.clr object from a "selex" data table
ALDEx2
3.6 years ago Greg • 0
0
votes
3
replies
3.4k
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Problem in kegga() and others getting data from KEGG after switch from http to https
limma KEGGREST EGSEA
updated 3.6 years ago by 4.3k • written 3.6 years ago by ★ 2.0k
0
votes
1
reply
1.1k
views
extendedSequences length is not the required for DeepCpf1 (34bp)
CRISPRseek
3.6 years ago Miguel • 0
3
votes
2
replies
15k
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ENSEMBL to ENTREZ ID
clusterProfiler
3.6 years ago martacrespi7 ▴ 10
0
votes
2
replies
901
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Error in NxtIRFcore
NxtIRFcore IRFinder
3.6 years ago ieki.tky • 0
4
votes
3
replies
3.4k
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Large difference between lfcshrink and non-shrunk DESeq2 results
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3.6 years ago Dave ▴ 10
0
votes
2
replies
1.1k
views
Get confused about the mean log-intensity (Amean)
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3.6 years ago OE • 0
1
vote
5
replies
2.3k
views
Unable to load mm10 genome for use with GenomicDistributions package
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3.6 years ago rashford • 0
0
votes
1
reply
1.4k
views
Pathview error Warning: Parsing ./mmu04928.xml file failed, please check the file!
KEGGgraph pathview
updated 3.6 years ago by ★ 4.1k • written 3.6 years ago by • 0
2
votes
2
replies
1.5k
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Can't load UCSC transcript IDs
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updated 3.6 years ago by ★ 4.1k • written 3.6 years ago by • 0
3
votes
3
replies
2.1k
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RFC: Inconsistent software license for scran & automated license checks
agpl license gpl scran
3.6 years ago • updated 3.5 years ago matthias-doering ▴ 40
0
votes
20
replies
3.7k
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Different DESeq2 results (both FC and pvalue) by changing col/row orders in input
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3.6 years ago Weisheng • 0
2
votes
4
replies
2.5k
views
deseq2 lfc shrinkage with few DEGs
RNASeq DESeq2
updated 10 months ago by 43k • written 3.6 years ago by ▴ 10
0
votes
3
replies
2.2k
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Persisting error in making a heatmap
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3.6 years ago beslinail • 0
3
votes
3
replies
1.5k
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Nested analysis or Collapsed-replicate analysis?
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updated 3.6 years ago by 43k • written 3.6 years ago by • 0
3
votes
9
replies
2.5k
views
How many features an ExpressionSet can contain ?
ExpressionSet
3.6 years ago OE • 0
0
votes
1
reply
794
views
Interpretation of comparison results in nested designs
DESeq2
updated 3.6 years ago by 43k • written 3.6 years ago by ▴ 10
1
vote
0
replies
3.2k
views
stuck on unimplemented type 'list' in 'EncodeElement'
list save dataframe
updated 3.6 years ago by 4.3k • written 3.6 years ago by ▴ 10
0
votes
2
replies
1.8k
views
I need cancer databases suggestion
#ccle #tcga #cancer
updated 3.6 years ago by 700 • written 3.6 years ago by • 0
2
votes
7
replies
2.4k
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batchelor correctExperiments() returns Error in eval(subscript, envir = eframe, enclos = eframe) : '...' used in an incorrect context
batchelor
3.6 years ago pcantalupo ▴ 10
2
votes
9
replies
4.3k
views
Stuck on how to voom-limma on RSEM data from TCGA
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3.6 years ago Peipei • 0
0
votes
1
reply
967
views
Check the CummeRbund PDF.
cummeRbund
updated 3.6 years ago by 4.3k • written 3.6 years ago by • 0
1
vote
5
replies
2.2k
views
Can't read in CEL files
GEO GEOquery
3.6 years ago OE • 0
0
votes
0
replies
1.4k
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Job: Bioinformatics Research Scientist- Epigenetics Group
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3.6 years ago xubeisi • 0
1
vote
3
replies
2.1k
views
Error in shrinkage for DESeq2
sva DESeq2
3.6 years ago Kent • 0
46,734 results • Page 85 of 935
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Comment: Changing multiple display parameters of a specific exon in GeneRegionTrack by TikTs3a3ssalpc • 0
In the Gviz package, individual exon styles like line width or font color are usually global, much like how the Massar Service centralizes …
Comment: limpa analysis advice by Gordon Smyth 53k
I prefer for limpa to work on precursor intensities, because my understanding is that precursors are the basic unit of identification and q…
Answer: Confirm that OpenStats will not be archived (pryr dependency) by shepherl 4.3k
As long as OpenStats is building cleanly and all needed stated dependencies are on CRAN or Bioconductor, OpenStats will not be archived. I…
Comment: Lowly expressed genes reported as significant when using lfcThreshold in DESeq by Michael Love 43k
Yes, I find that the LFC shrinkage and its corresponding stat `svalue` if you use lfcShrink with a threshold often returns more reliable ge…
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