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Creation
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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
792
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
902
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
1.2k
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
751
views
Adding chromosome numbers to the respective gene ids of DESeq2 output file
NewWave
hgu133a2.db
updated 23 days 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
849
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount
Rsubread
HPC
2.2 years ago
kthapa
• 0
0
votes
1
reply
840
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
2.8k
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
3.7k
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
917
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
786
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
1.5k
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 2.1 years ago by
Nat.Nataren
• 0 • written 2.2 years ago by
Ed Siefker
▴ 230
0
votes
3
replies
856
views
ukb Chromosomal position information was converted into SNPS
SNPediaR
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 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 2.2 years ago by
Alvin
• 0
1
vote
4
replies
1.3k
views
MDS plot edgeR
edgeR
updated 2.2 years ago by
Gordon Smyth
53k • written 2.2 years ago by
jbono
▴ 10
0
votes
10
replies
1.9k
views
ensembldb::getGenomeTwoBitFile() not working for many species
AnnotationHubSoftware
ensembldb
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 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 2.2 years ago by
xlu.cpu
• 0
0
votes
1
reply
928
views
T.fit function of maSigPro returns error message
maSigPro
2.2 years ago
hanna.g
• 0
1
vote
1
reply
1.5k
views
What MetaPhlAn3 database was used in cMD 3?
curatedMetagenomicData
updated 2.2 years ago by
Levi Waldron
★ 1.1k • written 2.2 years ago by
levlitichev
• 0
0
votes
4
replies
3.9k
views
pathview error "negative length vectors are not allowed
pathview
kegg
KEGG
updated 14 months ago by
Evan
• 0 • written 2.2 years ago by
Mauricio Diego
• 0
0
votes
3
replies
896
views
Technical Replicates in HTqPCR
HTqPCR
written 2.2 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 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
stuartthafass
• 0
3
votes
3
replies
3.5k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM
RNASeqData
DEAnalysis
limma
2.2 years ago
Ethan Nguyen
• 0
0
votes
1
reply
872
views
dmrseq and polymorphisms
dmrseq
updated 2.2 years ago by
keegan
▴ 60 • written 2.6 years ago by
giancarlo.castellano
• 0
0
votes
1
reply
737
views
TxDb.Dmelanogaster.UCSC.dm3.ensGene
TxDb.Dmelanogaster.UCSC.dm3.ensGene
updated 2.2 years ago by
ATpoint
★ 5.0k • written 2.2 years ago by
Gh
• 0
0
votes
3
replies
908
views
how to adjust other conditions when calling DEGs by DESeq2
DifferentialExpression
DESeq2
updated 2.2 years ago by
ATpoint
★ 5.0k • written 2.2 years ago by
xiaowen
• 0
1
vote
2
replies
2.0k
views
Should I use CPM or Voom transformed values for downstream analysis?
edgeR
limma
2.2 years ago
petertam1343
• 0
2
votes
1
reply
2.4k
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq
microbiome
Software
updated 2.2 years ago by
ATpoint
★ 5.0k • written 2.2 years ago by
HULFRED
▴ 10
0
votes
3
replies
993
views
The meaning of the analysis results when using a new metric in analysis
DESeq2
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
SH
▴ 10
1
vote
2
replies
917
views
RRID (unique searchable Research Resource Identifier ) of LymphoSeq
Clonality
2.2 years ago
Zijun
• 0
0
votes
0
replies
678
views
DTU analysis with factorial model
IsoformSwitchAnalyzeR
satuRn
2.2 years ago
jbono
▴ 10
1
vote
1
reply
1.6k
views
Can I transform already normalized rna-seq data with Z-score?
Z-score
RNASeqData
Deseq
DESeq2
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
khaserdene99
• 0
2
votes
3
replies
4.9k
views
TPM from STAR mapped counts
GeneExpression
GenomicFeatures
RNA-Seq
TPM
updated 2.2 years ago by
Gordon Smyth
53k • written 2.2 years ago by
gingergeiger22
• 0
3
votes
7
replies
1.7k
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 2.3 years ago by
Chris
▴ 20
0
votes
3
replies
1.2k
views
diffbind analyze for wheat
DiffBind
updated 21 months ago by
Igor
• 0 • written 2.2 years ago by
zgyu12
• 0
0
votes
1
reply
860
views
How to compared two groups out of twelve in DESeq2
DESeq2
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
paige.ramkissoon
• 0
46,693 results • Page
42 of 934
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Comment: Bioinformatician at the Lausanne University Hospital
by
eja.ger.m
• 0
For individuals looking to improve communication and collaboration in demanding medical or research environments like the Genetic Medicine …
Answer: NUPOP usage
by
shepherl
4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker?
by
fnfgame
• 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
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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