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16
views
Subsetting RNAseq data | voomaByGroup()
limma
13 hours ago
Anna
• 0
0
votes
0
replies
17
views
ERROR; return code from pthread_create() is 22
affy
13 hours ago
pickingastar
• 0
0
votes
0
replies
25
views
Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets
allele_freq
biomaRt
getBM
17 hours ago • updated 13 hours ago
Abiologist
• 0
0
votes
3
replies
91
views
STRINGdb : error with string_db$plot_network()
STRINGdb
updated 1 day ago by
damian.szk
▴ 80 • written 1 day ago by
ninidea
• 0
0
votes
0
replies
48
views
determine k during RUVSeq
RUVSeq
RUVnormalize
2 days ago
Ειρήνη
• 0
0
votes
0
replies
48
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
2 days ago
Shaimaa Gamal
• 0
0
votes
0
replies
14
views
Spam:
Unveiling Unmatched Best Custom Patches
SIMAT
2 days ago
oliverelijhan
0
0
votes
0
replies
64
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
2 days ago
Anton01
• 0
0
votes
0
replies
42
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
37
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
3 days ago
k200987
• 0
0
votes
0
replies
35
views
Difference in Contrast in DiffBind
DiffBind
3 days ago
zzrammal
• 0
0
votes
0
replies
51
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
4 days ago
Researcher
• 0
1
vote
2
replies
233
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
5 days ago • updated 2 days ago
BioinfGuru
▴ 30
0
votes
2
replies
97
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
5 days ago • updated 4 days ago
Yveto
• 0
0
votes
3
replies
174
views
ChAMP installation issue
Cha
ChAMP
5 days ago • updated 4 days ago
e1271094
• 0
0
votes
0
replies
74
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
9 days ago
neilzhao
▴ 30
2
votes
7
replies
380
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
10 days ago • updated 7 days ago
sajadahmad41454
• 0
0
votes
0
replies
72
views
Treeio as.treedata function seq lenght error
treeio
10 days ago
nromerov
• 0
0
votes
0
replies
90
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
12 days ago
Dinesh
• 0
0
votes
0
replies
118
views
dba.plotProfile() plotting and interpretation
DiffBind
15 days ago
Henry
▴ 10
0
votes
0
replies
98
views
flowStats for CyTOF
flowStats
16 days ago
tholmes
• 0
0
votes
0
replies
91
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
16 days ago
yvonneh
• 0
0
votes
0
replies
87
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
16 days ago
Ian D.
▴ 70
0
votes
3
replies
223
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 16 days ago by
ATpoint
★ 4.1k • written 17 days ago by
james.zhang20
• 0
0
votes
0
replies
139
views
Empty table plot using plotGseaTable()
fgsea
17 days ago • updated 15 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
19 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
23 days ago • updated 15 days ago
glaciya2018
• 0
0
votes
0
replies
99
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
24 days ago • updated 19 days ago
Sara
• 0
0
votes
0
replies
97
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
24 days ago
Dario Strbenac
★ 1.5k
0
votes
8
replies
385
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 23 days ago by
swbarnes2
★ 1.4k • written 25 days ago by
Aaliya
• 0
0
votes
2
replies
267
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
25 days ago • updated 23 days ago
shuwangxinze1996
• 0
2
votes
13
replies
481
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
27 days ago • updated 24 days ago
fernanda.backsouza
▴ 10
0
votes
0
replies
94
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
27 days ago
vaxahey107
• 0
0
votes
0
replies
105
views
I am trying to detect alternative splicing.
ASpli
28 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
240
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
266
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
4 weeks ago • updated 28 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
135
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
82
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
4 weeks ago
Henry
▴ 10
0
votes
1
reply
147
views
Deseq2 Rlog transformation
DESeq2
updated 4 weeks ago by
ATpoint
★ 4.1k • written 4 weeks ago by
Sahar
• 0
2
votes
2
replies
191
views
[DiffBind] Obtaining normalization factors
DiffBind
5 weeks ago • updated 4 weeks ago
Henry
▴ 10
0
votes
3
replies
286
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
104
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
5 weeks ago
Stevie Pederson
• 0
3
votes
6
replies
306
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
5 weeks ago
nhaus
▴ 30
0
votes
1
reply
196
views
DESeq2 gives an error and R crashes
DESeq2
5 weeks ago
Shefali
• 0
1,000 results • Page
1 of 20
Recent ...
Replies
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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