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0
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0
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445
views
flowStats for CyTOF
flowStats
20 months ago
tholmes
• 0
0
votes
0
replies
857
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
20 months ago
yvonneh
• 0
0
votes
0
replies
492
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
20 months ago
Ian D.
▴ 70
0
votes
3
replies
1.5k
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 20 months ago by
ATpoint
★ 5.0k • written 20 months ago by
james.zhang20
• 0
0
votes
0
replies
564
views
Empty table plot using plotGseaTable()
fgsea
20 months ago
Chris
▴ 20
0
votes
1
reply
1.2k
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
written 20 months ago by
Chris
▴ 20
0
votes
0
replies
778
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
20 months ago
glaciya2018
• 0
0
votes
0
replies
583
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
20 months ago
Sara
• 0
0
votes
0
replies
506
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
20 months ago
Dario Strbenac
★ 1.6k
0
votes
7
replies
2.8k
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 20 months ago by
swbarnes2
★ 1.4k • written 20 months ago by
Aaliya
• 0
0
votes
2
replies
971
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
20 months ago
shuwangxinze1996
• 0
5
votes
13
replies
4.3k
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
20 months ago
fernanda.backsouza
▴ 30
0
votes
0
replies
530
views
I am trying to detect alternative splicing.
ASpli
21 months ago
Sebashish
• 0
0
votes
0
replies
471
views
Warning while loading DEP package
DEP
updated 21 months ago by
shepherl
4.3k • written 21 months ago by
Namrata
• 0
1
vote
2
replies
1.0k
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
21 months ago
Le
• 0
1
vote
2
replies
772
views
Error in champ.load(): The following specified files do not exist
ChAMP
21 months ago
Sherin
• 0
0
votes
1
reply
466
views
Input Question for deseq.r
RSeqAn
updated 21 months ago by
ATpoint
★ 5.0k • written 21 months ago by
Nina
• 0
0
votes
4
replies
995
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
21 months ago
lonn
• 0
0
votes
0
replies
659
views
Enzyme Engineering
BioTIP
21 months ago
bocchemistry
• 0
0
votes
0
replies
422
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
21 months ago
Maliha Tabassum
• 0
0
votes
1
reply
616
views
what is the sampleFiles
chipseq
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
zhulin
• 0
0
votes
0
replies
562
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
21 months ago
Virangika
• 0
0
votes
0
replies
653
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
21 months ago
Henry
▴ 10
0
votes
1
reply
445
views
Deseq2 Rlog transformation
DESeq2
updated 21 months ago by
ATpoint
★ 5.0k • written 21 months ago by
Sahar
• 0
2
votes
2
replies
1.1k
views
[DiffBind] Obtaining normalization factors
DiffBind
21 months ago
Henry
▴ 10
0
votes
3
replies
1.8k
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 21 months ago by
W. Evan Johnson
▴ 870 • written 21 months ago by
schlumbohm
• 0
0
votes
0
replies
619
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
21 months ago
Stevie Pederson
• 0
3
votes
6
replies
1.7k
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
21 months ago
nhaus
▴ 70
0
votes
1
reply
788
views
DESeq2 gives an error and R crashes
DESeq2
21 months ago
Shefali
• 0
0
votes
0
replies
886
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
21 months ago
Eryn
• 0
0
votes
0
replies
532
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
21 months ago
Dennis
• 0
0
votes
2
replies
3.0k
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 4 months ago by
Andrea
• 0 • written 21 months ago by
Lucie
• 0
0
votes
0
replies
1.1k
views
ggtree tip label position (depth)
ggtree
21 months ago
Roope
• 0
2
votes
6
replies
4.5k
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
21 months ago
Chris
▴ 20
0
votes
0
replies
756
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
21 months ago
andromeda
• 0
0
votes
1
reply
658
views
Granges regionCounts not returning the expected number of entries
methylKit
21 months ago
Modoc Kesner
▴ 10
0
votes
0
replies
437
views
flowDensity on a flowset
flowDensity
21 months ago
fredrikwallberg
• 0
0
votes
0
replies
705
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
21 months ago
Macsue
• 0
0
votes
1
reply
988
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
ja569116
• 0
0
votes
2
replies
866
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
21 months ago
fer_talavera
• 0
0
votes
7
replies
2.4k
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
21 months ago
needNGS
• 0
0
votes
0
replies
670
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
21 months ago
feather-W
• 0
0
votes
0
replies
670
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
21 months ago
Ankit
▴ 20
1
vote
5
replies
1.3k
views
fgsea fork
fgsea
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
yimjohns
• 0
0
votes
0
replies
657
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
21 months ago
Pierre Lindenbaum
▴ 10
3
votes
3
replies
2.5k
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 21 months ago by
alan.ocallaghan
▴ 160 • written 21 months ago by
Najla Abassi
• 0
0
votes
0
replies
815
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
21 months ago
gshweta95
• 0
2
votes
2
replies
1.5k
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
written 21 months ago by
enee
▴ 10
0
votes
0
replies
503
views
Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
22 months ago
nromerov
• 0
1
vote
3
replies
855
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 22 months ago by
Marcel Ramos
700 • written 22 months ago by
Astrid Deschênes
• 0
1,000 results • Page
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Comment: Opportunity to host EuroBioC2026 Preconference workshops!
by
TikTsokaas33ocissalpc
• 0
Thank you for sharing the EuroBioC2026 workshop opportunity. I m interested in hosting a hands on session teaching reproducible data analys…
Comment: Ensembl plants at annotationHub?
by
jwp48
• 0
Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
Answer: Combining two proteomics datasets with limpa
by
Gordon Smyth
53k
Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
Comment: Guitar R package requires update due to dependency GenomicFeatures
by
ferran.llobet.cabau
▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub?
by
Guido Hooiveld
★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Votes
Answer: Where do the filename come from in the LOLA datasets?
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A: What is logFC and "B" in methylation analysis ??
limma moderated t-statistics and B-statistics
Comment: Guitar R package requires update due to dependency GenomicFeatures
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