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0
votes
0
replies
10
views
LRT, more than two conditions and pairwise comparisons
DESeq2
2 hours ago
boczniak767
▴ 720
0
votes
0
replies
10
views
How to run allelic imbalance in apeglm
apeglm
3 hours ago
euge.eugenio
▴ 20
0
votes
0
replies
19
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq
scRNAseq
9 hours ago
Bibi
• 0
0
votes
0
replies
31
views
ERROR; return code from pthread_create() is 22
affy
1 day ago • updated 12 hours ago
pickingastar
• 0
0
votes
0
replies
36
views
Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets
allele_freq
biomaRt
getBM
1 day ago • updated 12 hours ago
Abiologist
• 0
0
votes
3
replies
101
views
STRINGdb : error with string_db$plot_network()
STRINGdb
updated 2 days ago by
damian.szk
▴ 80 • written 2 days ago by
ninidea
• 0
0
votes
0
replies
50
views
determine k during RUVSeq
RUVSeq
RUVnormalize
3 days ago
Ειρήνη
• 0
0
votes
0
replies
51
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
3 days ago
Shaimaa Gamal
• 0
0
votes
0
replies
14
views
Spam:
Unveiling Unmatched Best Custom Patches
SIMAT
3 days ago
oliverelijhan
0
0
votes
0
replies
68
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
3 days ago
Anton01
• 0
0
votes
0
replies
45
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
3 days ago
danalvoronov
▴ 10
0
votes
0
replies
41
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
3 days ago
k200987
• 0
0
votes
0
replies
39
views
Difference in Contrast in DiffBind
DiffBind
4 days ago
zzrammal
• 0
0
votes
0
replies
55
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
5 days ago
Researcher
• 0
1
vote
2
replies
243
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
5 days ago • updated 3 days ago
BioinfGuru
▴ 30
0
votes
2
replies
103
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
6 days ago • updated 5 days ago
Yveto
• 0
0
votes
3
replies
180
views
ChAMP installation issue
Cha
ChAMP
6 days ago • updated 5 days ago
e1271094
• 0
0
votes
0
replies
80
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
9 days ago
neilzhao
▴ 30
2
votes
7
replies
389
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
11 days ago • updated 8 days ago
sajadahmad41454
• 0
0
votes
0
replies
75
views
Treeio as.treedata function seq lenght error
treeio
11 days ago
nromerov
• 0
0
votes
0
replies
94
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
12 days ago
Dinesh
• 0
0
votes
0
replies
122
views
dba.plotProfile() plotting and interpretation
DiffBind
16 days ago
Henry
▴ 10
0
votes
0
replies
99
views
flowStats for CyTOF
flowStats
17 days ago
tholmes
• 0
0
votes
0
replies
93
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
17 days ago
yvonneh
• 0
0
votes
0
replies
87
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
17 days ago
Ian D.
▴ 70
0
votes
3
replies
225
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 17 days ago by
ATpoint
★ 4.1k • written 17 days ago by
james.zhang20
• 0
0
votes
0
replies
140
views
Empty table plot using plotGseaTable()
fgsea
18 days ago • updated 16 days ago
Chris
▴ 10
0
votes
0
replies
95
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
20 days ago
Chris
▴ 10
0
votes
0
replies
143
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
24 days ago • updated 16 days ago
glaciya2018
• 0
0
votes
0
replies
99
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
25 days ago • updated 20 days ago
Sara
• 0
0
votes
0
replies
97
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
25 days ago
Dario Strbenac
★ 1.5k
0
votes
8
replies
387
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 24 days ago by
swbarnes2
★ 1.4k • written 26 days ago by
Aaliya
• 0
0
votes
2
replies
268
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
26 days ago • updated 24 days ago
shuwangxinze1996
• 0
2
votes
13
replies
483
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
28 days ago • updated 25 days ago
fernanda.backsouza
▴ 10
0
votes
0
replies
95
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
28 days ago
vaxahey107
• 0
0
votes
0
replies
106
views
I am trying to detect alternative splicing.
ASpli
29 days ago
Sebashish
• 0
0
votes
0
replies
134
views
Warning while loading DEP package
DEP
updated 4 weeks ago by
shepherl
3.9k • written 4 weeks ago by
Namrata
• 0
1
vote
2
replies
241
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
4 weeks ago
Le
• 0
1
vote
2
replies
180
views
Error in champ.load(): The following specified files do not exist
ChAMP
4 weeks ago
Sherin
• 0
0
votes
1
reply
112
views
Input Question for deseq.r
RSeqAn
updated 4 weeks ago by
ATpoint
★ 4.1k • written 4 weeks ago by
Nina
• 0
0
votes
4
replies
269
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
4 weeks ago • updated 29 days ago
lonn
• 0
0
votes
0
replies
92
views
Enzyme Engineering
BioTIP
4 weeks ago
bocchemistry
• 0
0
votes
0
replies
107
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
4 weeks ago
Maliha Tabassum
• 0
0
votes
1
reply
137
views
what is the sampleFiles
chipseq
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
zhulin
• 0
0
votes
0
replies
107
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
4 weeks ago
Virangika
• 0
0
votes
0
replies
85
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
4 weeks ago
Henry
▴ 10
0
votes
1
reply
149
views
Deseq2 Rlog transformation
DESeq2
updated 4 weeks ago by
ATpoint
★ 4.1k • written 5 weeks ago by
Sahar
• 0
2
votes
2
replies
193
views
[DiffBind] Obtaining normalization factors
DiffBind
5 weeks ago • updated 4 weeks ago
Henry
▴ 10
0
votes
3
replies
288
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 4 weeks ago by
W. Evan Johnson
▴ 850 • written 5 weeks ago by
schlumbohm
• 0
0
votes
0
replies
106
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
5 weeks ago
Stevie Pederson
• 0
1,000 results • Page
1 of 20
Recent ...
Replies
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
Galina
• 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
robersy
• 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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