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votes
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869
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Batch effect adjust in model matrix
BatchEffect
edgeR
updated 2.2 years ago by
ATpoint
★ 5.0k • written 2.2 years ago by
Giuseppe
• 0
0
votes
1
reply
712
views
HTSeqGenie runs very slow
HTSeqGenie
2.2 years ago
zh9118
• 0
0
votes
0
replies
824
views
Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno
ChIPSeq
MotifDiscovery
2.2 years ago
franciscrick41
• 0
5
votes
9
replies
2.8k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 20 months ago by
Gordon Smyth
53k • written 2.2 years ago by
Jonathan
▴ 10
0
votes
5
replies
1.2k
views
DESeq2, results(dds, name = <reference>) interpretation results
DESeq2
2.2 years ago
Rockbar
• 0
0
votes
2
replies
2.3k
views
For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor
clusterProfiler
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
nilanjanamani88
• 0
0
votes
1
reply
1.1k
views
Create design matrix for differential methylation analysis
Annotation
annotate
DifferentialMethylation
minfiDataEPIC
updated 2.2 years ago by
Basti
▴ 780 • written 2.2 years ago by
titangerd
• 0
0
votes
1
reply
800
views
Specifying evidence channels in STRINGdb
STRINGdb
stringdb
2.2 years ago
robynne.braun
• 0
0
votes
0
replies
1.3k
views
Variant Filtering on very large VCF files
VariantAnnotation
VariantFiltering
2.2 years ago
Bogdan
▴ 670
0
votes
3
replies
1.0k
views
Deseq2, multifactor model design for comparing adult Mutant mouse versus pup Mutant mouse with normalization to the age difference of the Wildtype co…
DGE
DESeq2
2.2 years ago
ruba-mahmoud
• 0
2
votes
2
replies
910
views
Remove duplicates of colData in TreeSummarizedExperiment
dplyr
TreeSummarizedExperiment
updated 2.2 years ago by
Michael Love
43k • written 2.2 years ago by
question_guy
• 0
0
votes
5
replies
1.3k
views
DeSeq2 design fails (full model matrix is less than full rank)
DESeq2
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
Theo
▴ 10
0
votes
2
replies
756
views
Adding chromosome numbers to the respective gene ids of DESeq2 output file
NewWave
hgu133a2.db
updated 4 weeks ago by
MurrayMertz
• 0 • written 2.2 years ago by
roy23032
• 0
5
votes
6
replies
1.4k
views
DataFrame Construction With Non-standard Column
S4Vectors
updated 2.2 years ago by
Hervé Pagès
16k • written 2.2 years ago by
Dario Strbenac
★ 1.6k
0
votes
0
replies
853
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount
Rsubread
HPC
2.2 years ago
kthapa
• 0
0
votes
1
reply
843
views
''Model_Matrix'' error
DifferentialExpression
limma
updated 2.2 years ago by
Gordon Smyth
53k • written 2.2 years ago by
Laghalelle
• 0
0
votes
2
replies
5.0k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq
featureCounts
ht-seq
written 5.4 years ago by
Arindam
▴ 80
1
vote
3
replies
2.5k
views
How does DESeq2 calculate FPKM values when gene lengths are not supplied?
deseq2
written 5.7 years ago by
hasse.bossenbroek
• 0
1
vote
3
replies
4.1k
views
SRAdb: Error downloading sqlite files
sradb
written 8.1 years ago by
arielle
• 0
2
votes
2
replies
2.1k
views
Matching Variants Between Two VCF Objects
VariantAnnotation
written 5.1 years ago by
Dario Strbenac
★ 1.6k
0
votes
4
replies
2.9k
views
how to save subsetted GDS file
gwastools
written 7.6 years ago by
Adrienne Stilp
▴ 30
0
votes
1
reply
12k
views
heatmap.2 - change column & row locations; angle / rotate
Cancer
Cancer
written 12.1 years ago by
Cheng, Yong-Sheng
▴ 10
0
votes
2
replies
1.3k
views
Rgraphviz installation: DLL problem?
Rgraphviz
Rgraphviz
written 15.9 years ago by
Gustavo Lacerda
▴ 10
1
vote
6
replies
3.8k
views
Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma
edger
timecourse
without replicate
voom
written 9.1 years ago by
Camila Orellana
▴ 10
1
vote
0
replies
1.7k
views
News:
Bioconductor 3.18 db0s, OrgDbs, and TxDbs now available
db0
release
Annotation
2.2 years ago
kayla.interdonato
▴ 160
0
votes
0
replies
576
views
Huge effect of a single sample on DEGs
limma
2.2 years ago
Jonathan
▴ 10
0
votes
4
replies
1.5k
views
filtering out lowly expressed genes by groups
RNASeqData
DESeq2
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
sohail.mbio
▴ 10
1
vote
1
reply
923
views
Why dbConnect GEOmetadb_demo.sqlite shows some information while dbConnect GEOmetadb.sqlite shows no information
GEOmetadb
GEOmetadb.sqlite
dbConnect
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
Lee
▴ 10
3
votes
4
replies
1.8k
views
DMRcate design
Epigenetics
EpigeneticsWorkflow
DMRcate
2.2 years ago
Jitendra
▴ 10
1
vote
1
reply
796
views
Further analysis after limma regression output
statistics
Epigenetics
limma
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
Jitendra
▴ 10
1
vote
6
replies
1.6k
views
DelayedArray::read_sparse_block
DelayedArray
updated 2.2 years ago by
Hervé Pagès
16k • written 2.3 years ago by
Koki
▴ 10
1
vote
5
replies
1.2k
views
Manual creation of qPCRset does not work
bug
nondetects
HTqPCR
updated 2.2 years ago by
Nat.Nataren
• 0 • written 2.3 years ago by
Ed Siefker
▴ 230
0
votes
3
replies
863
views
ukb Chromosomal position information was converted into SNPS
SNPediaR
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
wenbo
• 0
1
vote
3
replies
1.5k
views
Deseq2, enrichGO and ensembl ID
go
DESeq2
updated 11 months ago by
James W. MacDonald
68k • written 2.3 years ago by
Alvin
• 0
1
vote
4
replies
1.3k
views
MDS plot edgeR
edgeR
updated 2.3 years ago by
Gordon Smyth
53k • written 2.3 years ago by
jbono
▴ 10
0
votes
10
replies
2.0k
views
ensembldb::getGenomeTwoBitFile() not working for many species
AnnotationHubSoftware
ensembldb
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
cjag
• 0
0
votes
2
replies
2.9k
views
Bioconductor version cannot be validated
Bioconductor
updated 2.1 years ago by
Manuel
• 0 • written 2.3 years ago by
xlu.cpu
• 0
0
votes
1
reply
933
views
T.fit function of maSigPro returns error message
maSigPro
2.3 years ago
hanna.g
• 0
1
vote
1
reply
1.5k
views
What MetaPhlAn3 database was used in cMD 3?
curatedMetagenomicData
updated 2.3 years ago by
Levi Waldron
★ 1.1k • written 2.3 years ago by
levlitichev
• 0
0
votes
4
replies
4.0k
views
pathview error "negative length vectors are not allowed
pathview
kegg
KEGG
updated 14 months ago by
Evan
• 0 • written 2.3 years ago by
Mauricio Diego
• 0
0
votes
3
replies
904
views
Technical Replicates in HTqPCR
HTqPCR
written 2.3 years ago by
Ed Siefker
▴ 230
3
votes
3
replies
1.0k
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression
edgeR
limma
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
stuartthafass
• 0
3
votes
3
replies
3.6k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM
RNASeqData
DEAnalysis
limma
2.3 years ago
Ethan Nguyen
• 0
0
votes
1
reply
875
views
dmrseq and polymorphisms
dmrseq
updated 2.3 years ago by
keegan
▴ 60 • written 2.6 years ago by
giancarlo.castellano
• 0
0
votes
1
reply
740
views
TxDb.Dmelanogaster.UCSC.dm3.ensGene
TxDb.Dmelanogaster.UCSC.dm3.ensGene
updated 2.3 years ago by
ATpoint
★ 5.0k • written 2.3 years ago by
Gh
• 0
0
votes
3
replies
914
views
how to adjust other conditions when calling DEGs by DESeq2
DifferentialExpression
DESeq2
updated 2.3 years ago by
ATpoint
★ 5.0k • written 2.3 years ago by
xiaowen
• 0
1
vote
2
replies
2.1k
views
Should I use CPM or Voom transformed values for downstream analysis?
edgeR
limma
2.3 years ago
petertam1343
• 0
2
votes
1
reply
2.4k
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq
microbiome
Software
updated 2.3 years ago by
ATpoint
★ 5.0k • written 2.3 years ago by
HULFRED
▴ 10
0
votes
3
replies
996
views
The meaning of the analysis results when using a new metric in analysis
DESeq2
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
SH
▴ 10
1
vote
2
replies
920
views
RRID (unique searchable Research Resource Identifier ) of LymphoSeq
Clonality
2.3 years ago
Zijun
• 0
46,699 results • Page
42 of 934
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Comment: DESeq2 on non-RNASeq counts data
by
TikTsokaasocissalpc
• 0
In data analysis, behavior differences based on data type are common. Similarly, Best EDI Software adapts to non-standard transaction volum…
Comment: blockwiseModule crashes in the end and doesn't generate modules
by
gexose2839
• 0
Sounds good. @[time][1] [1]: https://timeduration.github.io
Comment: PFAM formats changed - is it still possible to use this with ISA?
by
TikTsokaasocissalpc
• 0
For mobile gaming enthusiasts, 3 Patti Lucky offers a seamless experience, unlike the frustration Harris faced with incompatible PFAM resul…
Answer: segfault in edgeR glmQLFit
by
Gordon Smyth
53k
Dear Mark, Thank you for providing a reproducible example. I confirm that I can reproduce the segfault myself on my own computer. The prob…
Answer: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
by
aqeel
• 0
Discover the pinnacle of Brazilian Jiu Jitsu gear at [Dragon][1] GI. [1]: https://dragongi.com/
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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