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0
votes
0
replies
13
views
flowStats for CyTOF
flowStats
8 hours ago
tholmes
• 0
0
votes
0
replies
17
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
10 hours ago
yvonneh
• 0
0
votes
0
replies
15
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
10 hours ago
Ian D.
▴ 70
0
votes
3
replies
93
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 15 hours ago by
ATpoint
★ 4.1k • written 1 day ago by
james.zhang20
• 0
0
votes
0
replies
55
views
Empty table plot using plotGseaTable()
fgsea
1 day ago
Chris
• 0
0
votes
0
replies
55
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
3 days ago
Chris
• 0
0
votes
0
replies
82
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools
TCGA
7 days ago
glaciya2018
• 0
0
votes
0
replies
72
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
8 days ago • updated 3 days ago
Sara
• 0
0
votes
0
replies
74
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
8 days ago
Dario Strbenac
★ 1.5k
0
votes
8
replies
323
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 7 days ago by
swbarnes2
★ 1.3k • written 9 days ago by
Aaliya
• 0
0
votes
2
replies
238
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
9 days ago • updated 7 days ago
shuwangxinze1996
• 0
1
vote
13
replies
370
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
11 days ago • updated 8 days ago
fernanda.backsouza
▴ 10
0
votes
0
replies
77
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
11 days ago
vaxahey107
• 0
0
votes
0
replies
91
views
I am trying to detect alternative splicing.
ASpli
12 days ago
Sebashish
• 0
0
votes
0
replies
114
views
Warning while loading DEP package
DEP
updated 14 days ago by
shepherl
3.9k • written 14 days ago by
Namrata
• 0
1
vote
2
replies
208
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
14 days ago
Le
• 0
1
vote
2
replies
150
views
Error in champ.load(): The following specified files do not exist
ChAMP
15 days ago • updated 14 days ago
Sherin
• 0
0
votes
1
reply
98
views
Input Question for deseq.r
RSeqAn
updated 14 days ago by
ATpoint
★ 4.1k • written 15 days ago by
Nina
• 0
0
votes
4
replies
229
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
15 days ago • updated 12 days ago
lonn
• 0
0
votes
0
replies
78
views
Enzyme Engineering
BioTIP
15 days ago
bocchemistry
• 0
0
votes
0
replies
88
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
16 days ago
Maliha Tabassum
• 0
0
votes
1
reply
118
views
what is the sampleFiles
chipseq
updated 16 days ago by
James W. MacDonald
65k • written 16 days ago by
zhulin
• 0
0
votes
0
replies
93
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
17 days ago
Virangika
• 0
0
votes
0
replies
70
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
17 days ago
Henry
▴ 10
0
votes
1
reply
128
views
Deseq2 Rlog transformation
DESeq2
updated 17 days ago by
ATpoint
★ 4.1k • written 18 days ago by
Sahar
• 0
2
votes
2
replies
166
views
[DiffBind] Obtaining normalization factors
DiffBind
20 days ago • updated 16 days ago
Henry
▴ 10
0
votes
3
replies
249
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 14 days ago by
W. Evan Johnson
▴ 850 • written 20 days ago by
schlumbohm
• 0
0
votes
0
replies
88
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
20 days ago
Stevie Pederson
• 0
3
votes
6
replies
265
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
21 days ago
nhaus
▴ 30
0
votes
1
reply
173
views
DESeq2 gives an error and R crashes
DESeq2
22 days ago • updated 21 days ago
Shefali
• 0
0
votes
0
replies
127
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
22 days ago
Eryn
• 0
0
votes
0
replies
85
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
22 days ago
Dennis
• 0
0
votes
1
reply
157
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 18 days ago by
Guido Hooiveld
★ 3.9k • written 22 days ago by
Lucie
• 0
0
votes
0
replies
106
views
ggtree tip label position (depth)
ggtree
23 days ago • updated 22 days ago
Roope
• 0
2
votes
6
replies
391
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
24 days ago
Chris
• 0
0
votes
0
replies
142
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
27 days ago
andromeda
• 0
0
votes
1
reply
127
views
Granges regionCounts not returning the expected number of entries
methylKit
28 days ago • updated 27 days ago
Modoc Kesner
▴ 10
0
votes
0
replies
98
views
flowDensity on a flowset
flowDensity
28 days ago
fredrikwallberg
• 0
0
votes
0
replies
88
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
28 days ago
Macsue
• 0
0
votes
1
reply
156
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
ja569116
• 0
0
votes
2
replies
288
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
4 weeks ago • updated 27 days ago
fer_talavera
• 0
0
votes
2
replies
253
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
4 weeks ago • updated 13 days ago
isaac.vock
• 0
0
votes
7
replies
387
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
4 weeks ago
needNGS
• 0
0
votes
0
replies
109
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
4 weeks ago
feather-W
• 0
0
votes
0
replies
109
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
4 weeks ago
Ankit
▴ 20
1
vote
5
replies
333
views
fgsea fork
fgsea
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
yimjohns
• 0
0
votes
0
replies
93
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
5 weeks ago
Pierre Lindenbaum
▴ 10
3
votes
3
replies
389
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 5 weeks ago by
alan.ocallaghan
▴ 160 • written 5 weeks ago by
Najla Abassi
• 0
0
votes
0
replies
116
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
5 weeks ago
gshweta95
• 0
2
votes
1
reply
209
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 5 weeks ago by
Guido Hooiveld
★ 3.9k • written 5 weeks ago by
enee
▴ 10
1,000 results • Page
1 of 20
Recent ...
Replies
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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