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0
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843
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DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
20 months ago
yvonneh
• 0
0
votes
0
replies
483
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
553
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
763
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
573
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
20 months ago
Sara
• 0
0
votes
0
replies
492
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
948
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
4.2k
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
20 months ago
fernanda.backsouza
▴ 30
0
votes
0
replies
526
views
I am trying to detect alternative splicing.
ASpli
20 months ago
Sebashish
• 0
0
votes
0
replies
465
views
Warning while loading DEP package
DEP
updated 20 months ago by
shepherl
4.2k • written 20 months ago by
Namrata
• 0
1
vote
2
replies
1.0k
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
20 months ago
Le
• 0
1
vote
2
replies
755
views
Error in champ.load(): The following specified files do not exist
ChAMP
20 months ago
Sherin
• 0
0
votes
1
reply
459
views
Input Question for deseq.r
RSeqAn
updated 20 months ago by
ATpoint
★ 5.0k • written 20 months ago by
Nina
• 0
0
votes
4
replies
981
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
20 months ago
lonn
• 0
0
votes
0
replies
658
views
Enzyme Engineering
BioTIP
20 months ago
bocchemistry
• 0
0
votes
0
replies
418
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
20 months ago
Maliha Tabassum
• 0
0
votes
1
reply
610
views
what is the sampleFiles
chipseq
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
zhulin
• 0
0
votes
0
replies
552
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
20 months ago
Virangika
• 0
0
votes
0
replies
640
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
20 months ago
Henry
▴ 10
0
votes
1
reply
439
views
Deseq2 Rlog transformation
DESeq2
updated 20 months ago by
ATpoint
★ 5.0k • written 20 months ago by
Sahar
• 0
2
votes
2
replies
1.1k
views
[DiffBind] Obtaining normalization factors
DiffBind
20 months ago
Henry
▴ 10
0
votes
3
replies
1.8k
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 20 months ago by
W. Evan Johnson
▴ 870 • written 20 months ago by
schlumbohm
• 0
0
votes
0
replies
613
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
20 months ago
Stevie Pederson
• 0
3
votes
6
replies
1.7k
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
20 months ago
nhaus
▴ 70
0
votes
1
reply
782
views
DESeq2 gives an error and R crashes
DESeq2
20 months ago
Shefali
• 0
0
votes
0
replies
848
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
20 months ago
Eryn
• 0
0
votes
0
replies
504
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
20 months ago
Dennis
• 0
0
votes
2
replies
2.9k
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 4 months ago by
Andrea
• 0 • written 20 months ago by
Lucie
• 0
0
votes
0
replies
1.0k
views
ggtree tip label position (depth)
ggtree
20 months ago
Roope
• 0
2
votes
6
replies
4.4k
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
20 months ago
Chris
▴ 20
0
votes
0
replies
745
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
636
views
Granges regionCounts not returning the expected number of entries
methylKit
21 months ago
Modoc Kesner
▴ 10
0
votes
0
replies
426
views
flowDensity on a flowset
flowDensity
21 months ago
fredrikwallberg
• 0
0
votes
0
replies
687
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
21 months ago
Macsue
• 0
0
votes
1
reply
967
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
852
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
2.3k
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
663
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
21 months ago
feather-W
• 0
0
votes
0
replies
651
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
641
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
21 months ago
Pierre Lindenbaum
▴ 10
3
votes
3
replies
2.4k
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
809
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
499
views
Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
21 months ago
nromerov
• 0
1
vote
3
replies
836
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 21 months ago by
Marcel Ramos
700 • written 21 months ago by
Astrid Deschênes
• 0
0
votes
0
replies
719
views
crlmm: CDF for Infinium Global Diversity Array By Illumina
globaldiversityarray
cdf
crlmm
21 months ago
mayra.haedo
• 0
1,000 results • Page
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Comment: Empty boxes in treemap plot rrvgo package
by
TikTsokaasocissalpc
• 0
Clear visualization matters just as much in mobile entertainment as in data analysis. The [Try KK33 Game App now][1] focuses on clean layou…
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by
adam80haynes
• 0
That's a fascinating application of 3D printing in a scientific context. Using this technology to create custom lab equipment, models of mo…
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by
TikTsokaasocissalpc
• 0
The Random Word Generator in Italian is a useful tool for generating ideas and exploring new approaches, much like the innovative research …
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• 0
If you want to share your research progress and microbiome discoveries with colleagues or friends, [snaptroid android][1] download free mak…
Answer: Limma-voom sample weights and impact on DEG numbers
by
Gordon Smyth
53k
I recommend that you always use voomLmFit() instead of the earlier voom() or voomWithQualityWeights() functions. Personally, I would use sa…
Votes
Answer: DESeq2 class error: superclass "ExpData" not defined in the environment of the o
Limma-voom sample weights and impact on DEG numbers
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
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Dario Strbenac
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