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2
votes
13
replies
480
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
27 days ago • updated 23 days ago
fernanda.backsouza
▴ 10
2
votes
7
replies
375
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
10 days ago • updated 7 days ago
sajadahmad41454
• 0
1
vote
3
replies
891
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 24 days ago by
Guangchuang Yu
★ 1.2k • written 14 months ago by
ruiqi.li
▴ 10
1
vote
2
replies
237
views
significant difference of p-values with dream() after updating VariancePartition
variancePartition
4 weeks ago • updated 29 days ago
Le
• 0
1
vote
2
replies
228
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
4 days ago • updated 1 day ago
BioinfGuru
▴ 30
0
votes
2
replies
96
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
5 days ago • updated 4 days ago
Yveto
• 0
0
votes
0
replies
142
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
73
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
8 days ago
neilzhao
▴ 30
0
votes
3
replies
173
views
ChAMP installation issue
Cha
ChAMP
5 days ago • updated 4 days ago
e1271094
• 0
0
votes
0
replies
96
views
flowStats for CyTOF
flowStats
16 days ago
tholmes
• 0
0
votes
2
replies
265
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
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
23
views
Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets
allele_freq
biomaRt
getBM
10 hours ago • updated 6 hours ago
Abiologist
• 0
0
votes
0
replies
117
views
dba.plotProfile() plotting and interpretation
DiffBind
15 days ago
Henry
▴ 10
0
votes
0
replies
36
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
2 days ago
k200987
• 0
0
votes
3
replies
88
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
99
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
24 days ago • updated 19 days ago
Sara
• 0
0
votes
3
replies
222
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 16 days ago by
ATpoint
★ 4.1k • written 16 days ago by
james.zhang20
• 0
0
votes
0
replies
14
views
Spam:
Unveiling Unmatched Best Custom Patches
SIMAT
2 days ago
oliverelijhan
0
0
votes
0
replies
90
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
16 days ago
yvonneh
• 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
0
replies
94
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
34
views
Difference in Contrast in DiffBind
DiffBind
3 days ago
zzrammal
• 0
0
votes
0
replies
46
views
determine k during RUVSeq
RUVSeq
RUVnormalize
2 days ago
Ειρήνη
• 0
0
votes
0
replies
46
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
2 days ago
Shaimaa Gamal
• 0
0
votes
0
replies
105
views
I am trying to detect alternative splicing.
ASpli
28 days ago
Sebashish
• 0
0
votes
0
replies
49
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
4 days ago
Researcher
• 0
0
votes
0
replies
62
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
2 days ago
Anton01
• 0
0
votes
0
replies
15
views
ERROR; return code from pthread_create() is 22
affy
5 hours ago
pickingastar
• 0
0
votes
0
replies
11
views
Subsetting RNAseq data | voomaByGroup()
limma
5 hours ago
Anna
• 0
0
votes
2
replies
282
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
6 weeks ago • updated 29 days ago
isaac.vock
• 0
0
votes
0
replies
71
views
Treeio as.treedata function seq lenght error
treeio
10 days ago
nromerov
• 0
0
votes
4
replies
265
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
136
views
Empty table plot using plotGseaTable()
fgsea
16 days ago • updated 14 days ago
Chris
▴ 10
0
votes
0
replies
85
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
16 days ago
Ian D.
▴ 70
0
votes
1
reply
1.3k
views
DSS CpG coverage threshold
DSS
WGBS
coverage
updated 9 days ago by
j.gilbert
• 0 • written 6.6 years ago by
floriandeckert
▴ 30
0
votes
0
replies
89
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
11 days ago
Dinesh
• 0
0
votes
0
replies
40
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
2 days ago
danalvoronov
▴ 10
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
39 results • Page
1 of 1
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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