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Views
Votes
0
votes
0
replies
22
views
LRT, pairwise comparisons and p-value adjustment
DESeq2
8 hours ago
boczniak767
▴ 720
0
votes
2
replies
173
views
Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
Biostrings
1 day ago • updated 16 hours ago
Ali Osman
• 0
0
votes
0
replies
33
views
gmapR source package contains x86_64 binaries
gmapR
1 day ago
Tom Lin
• 0
0
votes
1
reply
123
views
Error in render R qmd document (could not find function "process")
quantro
updated 1 day ago by
ATpoint
★ 4.2k • written 2 days ago by
Chutian
• 0
0
votes
2
replies
109
views
How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat
DESeq2
single-cell
scRNA
Pseudobulk
updated 1 day ago by
Guido Hooiveld
★ 4.0k • written 2 days ago by
Sara
• 0
0
votes
0
replies
39
views
conumee with Infinium MethylationEPIC v2.0
conumee
3 days ago
Maximus
• 0
0
votes
7
replies
205
views
Cannot install oligo on Fedora
oligo
source
Install
4 days ago • updated 8 hours ago
Guido Hooiveld
★ 4.0k
0
votes
4
replies
269
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq
Rsubread
updated 4 days ago by
Wei Shi
★ 3.6k • written 5 days ago by
atan
• 0
0
votes
0
replies
56
views
Problem in execuation of filterAndTrim command in DADA2
Bioconductor
dada2
6 days ago • updated 5 days ago
abhisek001
• 0
0
votes
0
replies
54
views
Conditional analysis
GENESIS
7 days ago
SuperDad
• 0
0
votes
0
replies
54
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq
peaks
ATAC
ChIPpeakAnno
7 days ago
Raghad
• 0
0
votes
0
replies
12
views
Spam:
Understanding Laser Hair Removal?
healthyControlsPresenceChecker
8 days ago
shahrozimmac
0
0
votes
0
replies
55
views
Processing of curatedmetagenomics
curatedMetagenomicData
9 days ago
Edward
• 0
0
votes
0
replies
67
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq
scRNAseq
9 days ago
Bibi
• 0
0
votes
0
replies
64
views
Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets
allele_freq
biomaRt
getBM
10 days ago • updated 9 days ago
Abiologist
• 0
0
votes
3
replies
162
views
STRINGdb : error with string_db$plot_network()
STRINGdb
updated 11 days ago by
damian.szk
▴ 80 • written 11 days ago by
ninidea
• 0
0
votes
0
replies
82
views
determine k during RUVSeq
RUVSeq
RUVnormalize
12 days ago
Ειρήνη
• 0
0
votes
0
replies
86
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
12 days ago
Shaimaa Gamal
• 0
0
votes
0
replies
16
views
Spam:
Unveiling Unmatched Best Custom Patches
SIMAT
12 days ago
oliverelijhan
0
0
votes
0
replies
102
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
12 days ago
Anton01
• 0
0
votes
0
replies
76
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
13 days ago
danalvoronov
▴ 10
0
votes
0
replies
71
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
13 days ago
k200987
• 0
0
votes
0
replies
69
views
Difference in Contrast in DiffBind
DiffBind
13 days ago
zzrammal
• 0
0
votes
0
replies
80
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
14 days ago
Researcher
• 0
1
vote
2
replies
287
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
15 days ago • updated 12 days ago
BioinfGuru
▴ 30
0
votes
2
replies
140
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
15 days ago • updated 14 days ago
Yveto
• 0
0
votes
7
replies
378
views
ChAMP installation issue
Cha
ChAMP
updated 6 days ago by
James W. MacDonald
66k • written 15 days ago by
e1271094
• 0
0
votes
0
replies
97
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
19 days ago
neilzhao
▴ 30
2
votes
7
replies
482
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
20 days ago • updated 17 days ago
sajadahmad41454
• 0
0
votes
0
replies
88
views
Treeio as.treedata function seq lenght error
treeio
21 days ago
nromerov
• 0
0
votes
0
replies
111
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
22 days ago
Dinesh
• 0
0
votes
0
replies
134
views
dba.plotProfile() plotting and interpretation
DiffBind
25 days ago
Henry
▴ 10
0
votes
0
replies
107
views
flowStats for CyTOF
flowStats
26 days ago
tholmes
• 0
0
votes
0
replies
105
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
26 days ago
yvonneh
• 0
0
votes
0
replies
100
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
26 days ago
Ian D.
▴ 70
0
votes
3
replies
251
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 26 days ago by
ATpoint
★ 4.2k • written 27 days ago by
james.zhang20
• 0
0
votes
0
replies
149
views
Empty table plot using plotGseaTable()
fgsea
27 days ago • updated 25 days ago
Chris
▴ 10
0
votes
0
replies
104
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
29 days ago
Chris
▴ 10
0
votes
0
replies
155
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
4 weeks ago • updated 25 days ago
glaciya2018
• 0
0
votes
0
replies
109
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
4 weeks ago • updated 29 days ago
Sara
• 0
0
votes
2
replies
239
views
Visium RNA
metaMSdata
written 10 weeks ago by
Karlison
• 0
1
vote
5
replies
1.7k
views
conumee with Infinium MethylationEPIC v2.0
MethylationEPICv2.0
conumee
updated 1 day ago by
sgomez
• 0 • written 14 months ago by
luca.s
▴ 50
0
votes
2
replies
773
views
Help with ENmix readidat
ENmix
IlluminaHumanMethylationEPICmanifest
updated 8 days ago by
James W. MacDonald
66k • written 2.1 years ago by
Daphna
• 0
4
votes
3
replies
1.0k
views
BayesSpace parameters for DLPFC Visium data
BayesSpace
written 3.1 years ago by
aspangl1
▴ 30
0
votes
1
reply
741
views
How to arrange multiple plots into one page in NOISeq?
noiseq
RNA-seq
quality control
updated 7 days ago by
baptiste.bidon
• 0 • written 4.8 years ago by
ag1805x
▴ 80
0
votes
1
reply
1.4k
views
DSS CpG coverage threshold
DSS
WGBS
coverage
updated 19 days ago by
j.gilbert
• 0 • written 6.6 years ago by
floriandeckert
▴ 30
46 results • Page
1 of 1
Recent ...
Replies
Answer: Counter-directional LFC shrinkage
by
swbarnes2
★ 1.4k
The y axes in those plots are logged. The average for condition1 is going to be higher than condition2 because of the very high outliers. …
Comment: Cannot install oligo on Fedora
by
Guido Hooiveld
★ 4.0k
Thanks for all suggestions and getting to the bottom of this! Unfortunately, fixing C code goes way above my skill level, so I cannot contr…
Comment: Cannot install oligo on Fedora
by
James W. MacDonald
66k
I think the solution is for the C code in `oligo` to be updated to work with more modern versions of `zlib`. The `zlibbioc` package is real…
Comment: Error in gseDO function
by
Guido Hooiveld
★ 4.0k
I don't fully understand what you are asking... Yet, in my opinion it doesn't make sense to use the results of only 12 genes for ORA (nor G…
Comment: Counter-directional LFC shrinkage
by
ATpoint
★ 4.2k
Is this RNA-seq? The unshrunken MA-plot looks very odd and indicates that normalization is completely offset.
Votes
A: DESeq2: add annotations (from data frame) to DESeqDataSet
Answer: Error in gseDO function
Comment: what the test method for enrichGO in clusterProfiler?
A: Comparison between two different group's pathway analysis results
DiffBind Batch Effect
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