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0
votes
0
replies
13
views
Error in champ.load(): The following specified files do not exist
ChAMP
1 hour ago
Sherin
• 0
0
votes
0
replies
11
views
Input Question for deseq.r
RSeqAn
3 hours ago
Nina
• 0
0
votes
0
replies
26
views
FilterByExpr low counts with small sample size
edgeR
5 hours ago • updated 2 hours ago
Jonathan
▴ 10
0
votes
0
replies
14
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
7 hours ago
lonn
• 0
0
votes
0
replies
22
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
7 hours ago • updated 5 hours ago
ussarizona
• 0
0
votes
0
replies
24
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
9 hours ago
quanah.hudson
• 0
0
votes
0
replies
16
views
Enzyme Engineering
BioTIP
12 hours ago
bocchemistry
• 0
0
votes
0
replies
38
views
covariate with negative and positive values
DESeq2
1 day ago
Brynn
• 0
0
votes
0
replies
28
views
Adding columns to DEXSeqResults object
DEXSeq
1 day ago
Clyde
• 0
0
votes
0
replies
34
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
1 day ago
Maliha Tabassum
• 0
0
votes
1
reply
58
views
what is the sampleFiles
chipseq
updated 1 day ago by
James W. MacDonald
65k • written 1 day ago by
zhulin
• 0
0
votes
0
replies
44
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
2 days ago
Virangika
• 0
0
votes
0
replies
34
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
2 days ago
Henry
▴ 10
0
votes
1
reply
78
views
Deseq2 Rlog transformation
DESeq2
updated 2 days ago by
ATpoint
★ 4.0k • written 3 days ago by
Sahar
• 0
2
votes
2
replies
121
views
[DiffBind] Obtaining normalization factors
DiffBind
5 days ago • updated 1 day ago
Henry
▴ 10
0
votes
0
replies
59
views
Cell type in SVD analysis
ChAMP
5 days ago
simleopold11
• 0
0
votes
2
replies
133
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
5 days ago • updated 1 day ago
schlumbohm
• 0
0
votes
0
replies
65
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
5 days ago
Stevie Pederson
• 0
3
votes
6
replies
195
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
6 days ago
nhaus
▴ 30
0
votes
1
reply
135
views
DESeq2 gives an error and R crashes
DESeq2
6 days ago • updated 5 days ago
Shefali
• 0
0
votes
0
replies
97
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
7 days ago
Eryn
• 0
0
votes
0
replies
65
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
7 days ago
Dennis
• 0
0
votes
1
reply
101
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 3 days ago by
Guido Hooiveld
★ 3.9k • written 7 days ago by
Lucie
• 0
0
votes
0
replies
78
views
ggtree tip label position (depth)
ggtree
8 days ago • updated 7 days ago
Roope
• 0
2
votes
6
replies
300
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
9 days ago
Chris
• 0
0
votes
0
replies
116
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
12 days ago
andromeda
• 0
0
votes
1
reply
104
views
Granges regionCounts not returning the expected number of entries
methylKit
12 days ago
Modoc Kesner
▴ 10
0
votes
0
replies
74
views
flowDensity on a flowset
flowDensity
13 days ago
fredrikwallberg
• 0
0
votes
0
replies
67
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
13 days ago
Macsue
• 0
0
votes
1
reply
124
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 15 days ago by
James W. MacDonald
65k • written 16 days ago by
ja569116
• 0
0
votes
2
replies
254
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
17 days ago • updated 12 days ago
fer_talavera
• 0
0
votes
1
reply
190
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
updated 8 days ago by
Wei Shi
★ 3.6k • written 17 days ago by
isaac.vock
• 0
0
votes
7
replies
304
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
18 days ago • updated 15 days ago
needNGS
• 0
0
votes
0
replies
90
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
19 days ago
feather-W
• 0
0
votes
0
replies
85
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
19 days ago
Ankit
▴ 20
1
vote
5
replies
281
views
fgsea fork
fgsea
updated 19 days ago by
James W. MacDonald
65k • written 19 days ago by
yimjohns
• 0
0
votes
0
replies
75
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
20 days ago
Pierre Lindenbaum
▴ 10
3
votes
3
replies
319
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 23 days ago by
alan.ocallaghan
▴ 160 • written 24 days ago by
Najla Abassi
• 0
0
votes
0
replies
95
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
23 days ago
gshweta95
• 0
2
votes
1
reply
173
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 24 days ago by
Guido Hooiveld
★ 3.9k • written 26 days ago by
enee
▴ 10
0
votes
0
replies
95
views
Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
26 days ago
nromerov
• 0
1
vote
3
replies
228
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 26 days ago by
Marcel Ramos
690 • written 27 days ago by
Astrid Deschênes
• 0
0
votes
0
replies
105
views
crlmm: CDF for Infinium Global Diversity Array By Illumina
globaldiversityarray
cdf
crlmm
28 days ago
mayra.haedo
• 0
0
votes
0
replies
97
views
Macsquant FCS in read.FCS & opencyto
FlowCytometry
flowWorkspace
flowCore
28 days ago
taylor.witte
• 0
0
votes
0
replies
116
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
28 days ago
erbrocato
• 0
1
vote
4
replies
240
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
28 days ago • updated 27 days ago
samuel.channon
• 0
0
votes
2
replies
174
views
Visium RNA
metaMSdata
updated 28 days ago by
vvvc360work2
• 0 • written 29 days ago by
Karlison
• 0
1
vote
2
replies
234
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 28 days ago by
ATpoint
★ 4.0k • written 29 days ago by
maximilian.beikirch
• 0
0
votes
0
replies
101
views
DNAcopy segment function not reproducible even when setting seed
DNAcopy
29 days ago
BID
• 0
1
vote
3
replies
236
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 20 days ago by
mercedeh.movassagh
▴ 10 • written 29 days ago by
María
• 0
1,000 results • Page
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Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with doctor know about Alzheimer and they don't expect significan…
Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Comment: Methylation Analysis experiment design using Limma
by
hortense96
• 0
Hi, Thank you very much for your answer. It's true that I only used 6 samples for this analysis, which is consistent with your explanation…
Comment: Error using champ.import
by
shilpa
• 0
I'm having same issues too. Did anyone manage to resolve it?
Answer: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
You don't explain how many samples you have (columns of data), but the warning message shown in your post would arise if there are in fact …
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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