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0
votes
0
replies
4
views
Create design matrix for differential methylation analysis
Annotation
annotate
DifferentialMethylation
minfiDataEPIC
41 minutes ago
titangerd
• 0
11
votes
4
replies
1.4k
views
LIMMA dupcor() function time issue.
limma
microarray
block
updated 1 hour ago by
Gordon Smyth
48k • written 4.6 years ago by
tleona3
• 0
0
votes
1
reply
14
views
Specifying evidence channels in STRINGdb
STRINGdb
stringdb
2 hours ago
robynne.braun
• 0
0
votes
1
reply
2.0k
views
Problems with FLOWAI
flowAI
updated 3 hours ago by
SHASHI
• 0 • written 2.4 years ago by
msoares
• 0
0
votes
0
replies
12
views
Variant Filtering on very large VCF files
VariantAnnotation
VariantFiltering
5 hours ago
Bogdan
▴ 660
1
vote
6
replies
117
views
DataFrame Construction With Non-standard Column
S4Vectors
updated 5 hours ago by
Hervé Pagès
16k • written 1 day ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
85
views
Deseq2, how to model design for comparing Mutant mouse at age 14 days versus Mutant mouse at birth with normalization to the age difference of the W…
DESeq2
DGE
updated 6 hours ago by
swbarnes2
★ 1.3k • written 13 hours ago by
ruba-mahmoud
• 0
0
votes
2
replies
47
views
Remove duplicates of colData in TreeSummarizedExperiment
dplyr
TreeSummarizedExperiment
updated 6 hours ago by
Michael Love
40k • written 9 hours ago by
question_guy
• 0
0
votes
3
replies
45
views
DeSeq2 design fails (full model matrix is less than full rank)
DESeq2
updated 8 hours ago by
Basti
▴ 720 • written 10 hours ago by
Theo
• 0
0
votes
2
replies
28
views
Adding chromosome numbers to the respective gene ids of DESeq2 output file
NewWave
hgu133a2.db
updated 10 hours ago by
ATpoint
★ 3.4k • written 15 hours ago by
roy23032
• 0
0
votes
2
replies
2.9k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq
featureCounts
ht-seq
written 3.2 years ago by
ag1805x
▴ 80
0
votes
0
replies
19
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount
Rsubread
HPC
20 hours ago
kthapa
• 0
0
votes
1
reply
80
views
''Model_Matrix'' error
DifferentialExpression
limma
updated 1 day ago by
Gordon Smyth
48k • written 2 days ago by
Laghalelle
• 0
2
votes
11
replies
1.1k
views
Speeding up of DelayedArray::write_block()
HDF5Array
DelayedArray
2.0 years ago • updated 1 day ago
Koki
▴ 10
1
vote
6
replies
324
views
DelayedArray::read_sparse_block
DelayedArray
updated 1 day ago by
Hervé Pagès
16k • written 5 weeks ago by
Koki
▴ 10
3
votes
4
replies
152
views
DMRcate design
Epigenetics
EpigeneticsWorkflow
DMRcate
3 days ago • updated 2 days ago
Jitendra
▴ 10
8
votes
8
replies
7.8k
views
Steps needed to change design (relevel factors) in DESeq2
deseq2
DESeq2
updated 3 days ago by
jd774
• 0 • written 4.2 years ago by
krassowski.michal
▴ 40
0
votes
0
replies
93
views
Huge effect of a single sample on DEGs
limma
3 days ago
Jonathan
• 0
1
vote
3
replies
1.3k
views
How does DESeq2 calculate FPKM values when gene lengths are not supplied?
deseq2
written 3.5 years ago by
hasse.bossenbroek
• 0
1
vote
3
replies
2.9k
views
SRAdb: Error downloading sqlite files
sradb
written 5.9 years ago by
arielle
• 0
0
votes
2
replies
495
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 5 months ago by
mauricio.microbiol
• 0
2
votes
2
replies
963
views
Matching Variants Between Two VCF Objects
VariantAnnotation
written 2.8 years ago by
Dario Strbenac
★ 1.5k
0
votes
4
replies
1.4k
views
how to save subsetted GDS file
gwastools
written 5.4 years ago by
Adrienne Stilp
▴ 30
0
votes
1
reply
10k
views
heatmap.2 - change column & row locations; angle / rotate
Cancer
Cancer
written 9.9 years ago by
Cheng, Yong-Sheng
▴ 10
0
votes
2
replies
715
views
Rgraphviz installation: DLL problem?
Rgraphviz
Rgraphviz
written 13.7 years ago by
Gustavo Lacerda
▴ 10
1
vote
6
replies
2.2k
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 6.9 years ago by
Camila Orellana
▴ 10
1
vote
0
replies
37
views
News:
Bioconductor 3.18 db0s, OrgDbs, and TxDbs now available
db0
release
Annotation
3 days ago
kayla.interdonato
150
0
votes
4
replies
167
views
filtering out lowly expressed genes by groups
RNASeqData
DESeq2
updated 3 days ago by
James W. MacDonald
63k • written 3 days ago by
sohail.mbio
▴ 10
0
votes
3
replies
481
views
Representation of self-loops and the calculation of degrees
graph
updated 3 days ago by
Vincent J. Carey, Jr.
6.7k • written 9 months ago by
Szabolcs
• 0
0
votes
1
reply
72
views
Why dbConnect GEOmetadb_demo.sqlite shows some information while dbConnect GEOmetadb.sqlite shows no information
GEOmetadb
GEOmetadb.sqlite
dbConnect
updated 3 days ago by
James W. MacDonald
63k • written 3 days ago by
Lee
• 0
1
vote
1
reply
68
views
Further analysis after limma regression output
statistics
Epigenetics
limma
updated 3 days ago by
James W. MacDonald
63k • written 3 days ago by
Jitendra
▴ 10
1
vote
8
replies
968
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
Bioconductor
Devel
devel
updated 3 days ago by
Hervé Pagès
16k • written 3 months ago by
shepherl
3.5k
1
vote
2
replies
95
views
Manual creation of qPCRset does not work
bug
nondetects
HTqPCR
4 days ago
Ed Siefker
▴ 230
0
votes
3
replies
119
views
ukb Chromosomal position information was converted into SNPS
SNPediaR
updated 4 days ago by
James W. MacDonald
63k • written 5 days ago by
wenbo
• 0
0
votes
1
reply
126
views
T.fit function of maSigPro returns error message
maSigPro
5 days ago • updated 4 days ago
hanna.g
• 0
1
vote
1
reply
72
views
Deseq2, enrichGO and ensembl ID
go
DESeq2
updated 4 days ago by
James W. MacDonald
63k • written 4 days ago by
Alvin
• 0
1
vote
4
replies
147
views
MDS plot edgeR
edgeR
updated 4 days ago by
Gordon Smyth
48k • written 5 days ago by
jbono
▴ 10
0
votes
1
reply
1.2k
views
Doubts regarding Pathview
Annotation
pathview
Annotation
pathview
written 9.2 years ago by
Luo Weijun
★ 1.6k
0
votes
3
replies
126
views
Technical Replicates in HTqPCR
HTqPCR
written 6 days ago by
Ed Siefker
▴ 230
1
vote
3
replies
1.4k
views
Combining and using 10x Genomics output in SingleCellExperiment Objects
SingleCellExperiment
written 4.5 years ago by
Matthew Thornton
▴ 350
3
votes
10
replies
549
views
Timely differentially expressed genes
timecoursedata
limma
updated 5 days ago by
Gordon Smyth
48k • written 19 days ago by
triZZla
• 0
0
votes
10
replies
223
views
ensembldb::getGenomeTwoBitFile() not working for many species
AnnotationHubSoftware
ensembldb
updated 5 days ago by
James W. MacDonald
63k • written 5 days ago by
cjag
• 0
0
votes
0
replies
60
views
Bioconductor version cannot be validated
Bioconductor
5 days ago
xlu.cpu
• 0
3
votes
3
replies
164
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression
edgeR
limma
updated 5 days ago by
James W. MacDonald
63k • written 6 days ago by
stuartthafass
• 0
0
votes
6
replies
318
views
annotation EpicV2
minfiDataEPIC
EpicV2
updated 5 days ago by
Zuguang Gu
▴ 240 • written 4 weeks ago by
Izabela.ams
• 0
1
vote
1
reply
79
views
What MetaPhlAn3 database was used in cMD 3?
curatedMetagenomicData
updated 5 days ago by
Levi Waldron
1.1k • written 7 days ago by
levlitichev
• 0
3
votes
3
replies
399
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM
RNASeqData
DEAnalysis
limma
6 days ago • updated 5 days ago
Ethan Nguyen
• 0
0
votes
0
replies
42
views
pathview error "negative length vectors are not allowed
pathview
kegg
KEGG
6 days ago
Mauricio Diego
• 0
0
votes
3
replies
176
views
The meaning of the analysis results when using a new metric in analysis
DESeq2
updated 6 days ago by
James W. MacDonald
63k • written 7 days ago by
SH
• 0
3
votes
7
replies
352
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 12 days ago by
Chris
• 0
44,772 results • Page
1 of 896
Recent ...
Replies
Comment: LIMMA dupcor() function time issue.
by
Gordon Smyth
48k
That's ok, but there is nothing to be gained by subsetting 1000 times. It would be better to simply subset 100,000 rows once, although the …
Comment: Specifying evidence channels in STRINGdb
by
robynne.braun
• 0
Also I found prior thread here addressing the same question with response that functionality will be supported someday. This was a few year…
Comment: Problems with FLOWAI
by
SHASHI
• 0
please try this using short path name and keeping your fcs file and wsp file in your local directory https://youtu.be/xLeqE7PNYzA
Comment: DataFrame Construction With Non-standard Column
by
Hervé Pagès
16k
SimpleList is a List derivative and List derivatives in general don't need protection. For example, a GRangesList object (which is also a L…
Answer: Deseq2, how to model design for comparing Mutant mouse at age 14 days versus Mu
by
swbarnes2
★ 1.3k
The Status grouping you show above is good to use if you want to simply compare one subset of samples to another subset. The ~Genotype +…
Votes
Answer: Deseq2, enrichGO and ensembl ID
A: LIMMA dupcor() function time issue.
A: LIMMA dupcor() function time issue.
Answer: Further analysis after limma regression output
A: collapseReplicates in DESeq2
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