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Votes
3
votes
6
replies
270
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
23 days ago
nhaus
▴ 30
2
votes
2
replies
171
views
[DiffBind] Obtaining normalization factors
DiffBind
22 days ago • updated 18 days ago
Henry
▴ 10
2
votes
6
replies
398
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
26 days ago
Chris
• 0
1
vote
2
replies
157
views
Error in champ.load(): The following specified files do not exist
ChAMP
17 days ago • updated 16 days ago
Sherin
• 0
1
vote
3
replies
858
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 10 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
1
vote
13
replies
395
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
13 days ago • updated 10 days ago
fernanda.backsouza
▴ 10
1
vote
2
replies
210
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
16 days ago
Le
• 0
1
vote
7
replies
1.8k
views
Error using champ.import
ChAMP
EPICv2
updated 17 days ago by
shilpa
• 0 • written 10 months ago by
medha.suman
• 0
0
votes
0
replies
40
views
Handling multiple differential expression comparisons
DESeq2
1 day ago
Zainab
• 0
0
votes
0
replies
91
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
22 days ago
Stevie Pederson
• 0
0
votes
0
replies
94
views
I am trying to detect alternative splicing.
ASpli
14 days ago
Sebashish
• 0
0
votes
8
replies
341
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 10 days ago by
swbarnes2
★ 1.3k • written 11 days ago by
Aaliya
• 0
0
votes
0
replies
81
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
14 days ago
vaxahey107
• 0
0
votes
0
replies
85
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
10 days ago • updated 5 days ago
Sara
• 0
0
votes
0
replies
69
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
5 days ago
Chris
• 0
0
votes
0
replies
71
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
19 days ago
Henry
▴ 10
0
votes
0
replies
79
views
Empty table plot using plotGseaTable()
fgsea
3 days ago • updated 1 day ago
Chris
• 0
0
votes
0
replies
92
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
18 days ago
Maliha Tabassum
• 0
0
votes
3
replies
253
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 16 days ago by
W. Evan Johnson
▴ 850 • written 22 days ago by
schlumbohm
• 0
0
votes
0
replies
36
views
dba.plotProfile() plotting and interpretation
DiffBind
1 day ago
Henry
▴ 10
0
votes
0
replies
108
views
ggtree tip label position (depth)
ggtree
25 days ago • updated 24 days ago
Roope
• 0
0
votes
0
replies
130
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
24 days ago
Eryn
• 0
0
votes
1
reply
157
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 20 days ago by
Guido Hooiveld
★ 3.9k • written 24 days ago by
Lucie
• 0
0
votes
1
reply
342
views
Gene names from Matrix
BioCor
StarBioTrek
MatrixGenerics
updated 24 days ago by
Lluís Revilla Sancho
▴ 730 • written 7 months ago by
karmasstark
• 0
0
votes
1
reply
510
views
Cibersort phenotype file
cibersort
deconvR
immune
updated 25 days ago by
ivorychan7777
• 0 • written 15 months ago by
609b0d25
• 0
0
votes
1
reply
98
views
Input Question for deseq.r
RSeqAn
updated 16 days ago by
ATpoint
★ 4.1k • written 17 days ago by
Nina
• 0
0
votes
1
reply
553
views
CopywriteR output
CopywriteR
updated 29 days ago by
fer_talavera
• 0 • written 2.5 years ago by
Joshua
• 0
0
votes
1
reply
174
views
DESeq2 gives an error and R crashes
DESeq2
24 days ago • updated 23 days ago
Shefali
• 0
0
votes
0
replies
118
views
Warning while loading DEP package
DEP
updated 16 days ago by
shepherl
3.9k • written 16 days ago by
Namrata
• 0
0
votes
0
replies
41
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
2 days ago
yvonneh
• 0
0
votes
4
replies
235
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
17 days ago • updated 14 days ago
lonn
• 0
0
votes
1
reply
130
views
Deseq2 Rlog transformation
DESeq2
updated 19 days ago by
ATpoint
★ 4.1k • written 21 days ago by
Sahar
• 0
0
votes
0
replies
35
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
2 days ago
Ian D.
▴ 70
0
votes
1
reply
130
views
Granges regionCounts not returning the expected number of entries
methylKit
4 weeks ago • updated 29 days ago
Modoc Kesner
▴ 10
0
votes
0
replies
36
views
flowStats for CyTOF
flowStats
2 days ago
tholmes
• 0
0
votes
2
replies
242
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
12 days ago • updated 9 days ago
shuwangxinze1996
• 0
0
votes
2
replies
255
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
4 weeks ago • updated 15 days ago
isaac.vock
• 0
0
votes
0
replies
80
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
10 days ago
Dario Strbenac
★ 1.5k
0
votes
1
reply
119
views
what is the sampleFiles
chipseq
updated 18 days ago by
James W. MacDonald
65k • written 18 days ago by
zhulin
• 0
0
votes
0
replies
80
views
Enzyme Engineering
BioTIP
17 days ago
bocchemistry
• 0
0
votes
0
replies
143
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
29 days ago
andromeda
• 0
0
votes
0
replies
115
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
9 days ago • updated 1 day ago
glaciya2018
• 0
0
votes
3
replies
117
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 2 days ago by
ATpoint
★ 4.1k • written 3 days ago by
james.zhang20
• 0
0
votes
2
replies
296
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 29 days ago
fer_talavera
• 0
0
votes
0
replies
23
views
fgsea significant result
fgsea
6 hours ago
Chris
• 0
0
votes
0
replies
85
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
24 days ago
Dennis
• 0
0
votes
0
replies
94
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
19 days ago
Virangika
• 0
47 results • Page
1 of 1
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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