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144
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One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
25 days ago • updated 17 days ago
glaciya2018
• 0
0
votes
2
replies
170
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
20 days ago • updated 17 days ago
Aurora
• 0
0
votes
4
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 3 days ago by
angelaesper43
• 0 • written 19 months ago by
Maria Doyle
▴ 70
0
votes
5
replies
2.9k
views
DNAString: Standard checksum function?
Biostrings
FASTA
sequencing
8.2 years ago • updated 14 days ago
Henrik Bengtsson
★ 2.4k
0
votes
0
replies
12
views
Spam:
Understanding Laser Hair Removal?
healthyControlsPresenceChecker
9 hours ago
shahrozimmac
0
0
votes
0
replies
87
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
10 days ago
neilzhao
▴ 30
0
votes
5
replies
140
views
all variables in design formula must be columns in colData (Deseq2) error
BatchQC
batchinDeseq2.
columnsincolData.
1 day ago • updated 5 hours ago
Galina
• 0
0
votes
1
reply
114
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 11 days ago by
ATpoint
★ 4.1k • written 11 days ago by
sajadahmad41454
• 0
0
votes
4
replies
141
views
error running enricher from clusterprofiler
clusterProfiler
cluster
5 days ago • updated 4 days ago
Yael
• 0
0
votes
0
replies
99
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
13 days ago
Dinesh
• 0
0
votes
5
replies
325
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 26 days ago by
James W. MacDonald
65k • written 28 days ago by
Gayatri
• 0
0
votes
1
reply
141
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 18 days ago by
4r-rtg
• 0
0
votes
3
replies
191
views
ChAMP installation issue
Cha
ChAMP
7 days ago • updated 6 days ago
e1271094
• 0
0
votes
0
replies
100
views
flowStats for CyTOF
flowStats
18 days ago
tholmes
• 0
0
votes
6
replies
305
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 16 days ago by
swbarnes2
★ 1.4k • written 17 days ago by
arfranco
▴ 130
0
votes
1
reply
181
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 10 days ago by
ATpoint
★ 4.1k • written 10 days ago by
sajadahmad41454
• 0
0
votes
0
replies
48
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
4 days ago
k200987
• 0
0
votes
0
replies
55
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
4 days ago
Shaimaa Gamal
• 0
0
votes
8
replies
519
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
updated 5 days ago by
BioinfGuru
▴ 30 • written 6 days ago by
Eric Katagirya
• 0
0
votes
0
replies
142
views
Empty table plot using plotGseaTable()
fgsea
18 days ago • updated 16 days ago
Chris
▴ 10
0
votes
2
replies
955
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 5 days ago by
mariakenneth147
• 0 • written 18 months ago by
pharamac
• 0
0
votes
1
reply
46
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC
BatchEffect
RNASeq
updated 3 hours ago by
James W. MacDonald
65k • written 11 hours ago by
ttt
• 0
0
votes
44
replies
3.2k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
updated 6 days ago by
Michael Love
42k • written 15 months ago by
Poonam
• 0
0
votes
1
reply
1.3k
views
DSS CpG coverage threshold
DSS
WGBS
coverage
updated 11 days ago by
j.gilbert
• 0 • written 6.6 years ago by
floriandeckert
▴ 30
0
votes
0
replies
43
views
Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets
allele_freq
biomaRt
getBM
2 days ago • updated 1 day ago
Abiologist
• 0
0
votes
0
replies
124
views
dba.plotProfile() plotting and interpretation
DiffBind
17 days ago
Henry
▴ 10
0
votes
1
reply
138
views
FDR via q-value
qvalue
updated 28 days ago by
James W. MacDonald
65k • written 4 weeks ago by
John
• 0
0
votes
3
replies
114
views
STRINGdb : error with string_db$plot_network()
STRINGdb
updated 3 days ago by
damian.szk
▴ 80 • written 3 days ago by
ninidea
• 0
0
votes
1
reply
174
views
ATACseq merge peaks
DiffBind
updated 24 days ago by
ATpoint
★ 4.1k • written 26 days ago by
Shloka
• 0
0
votes
0
replies
83
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
4 days ago
Anton01
• 0
0
votes
0
replies
55
views
determine k during RUVSeq
RUVSeq
RUVnormalize
4 days ago
Ειρήνη
• 0
0
votes
0
replies
31
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq
scRNAseq
1 day ago
Bibi
• 0
0
votes
0
replies
48
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
4 days ago
danalvoronov
▴ 10
0
votes
3
replies
228
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 18 days ago by
ATpoint
★ 4.1k • written 18 days ago by
james.zhang20
• 0
0
votes
0
replies
15
views
Spam:
Unveiling Unmatched Best Custom Patches
SIMAT
4 days ago
oliverelijhan
0
0
votes
1
reply
37
views
Control group between 2 batches have different expression in RNAseq data
BatchQC
BatchEffect
rnaseqGene
Normalization
updated 3 hours ago by
James W. MacDonald
65k • written 9 hours ago by
Đình Vinh
• 0
0
votes
1
reply
37
views
LRT, more than two conditions and pairwise comparisons
DESeq2
updated 3 hours ago by
James W. MacDonald
65k • written 23 hours ago by
boczniak767
▴ 720
0
votes
1
reply
38
views
ENCORI or starBase : ceRNA data retrieval using Web API and curl
curl
microRNA
starBase
webapi
ENCORI
updated 7 hours ago by
ATpoint
★ 4.1k • written 8 hours ago by
V_Vibes
• 0
0
votes
3
replies
234
views
Couldn't connect to server while using "pathways"
graphite
updated 13 days ago by
Michael Love
42k • written 14 days ago by
fduguchunhui
• 0
0
votes
1
reply
124
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 20 days ago by
shepherl
3.9k • written 20 days ago by
bounlu
• 0
0
votes
2
replies
116
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
4 days ago • updated 3 days ago
makala
• 0
0
votes
3
replies
3.7k
views
[Mfuzz] Error in cmeans(exprs(eset)
Mfuzz
Mfuzz
updated 13 days ago by
Caio
• 0 • written 13.1 years ago by
boczniak767
▴ 720
0
votes
1
reply
139
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 20 days ago by
Michael Love
42k • written 20 days ago by
Agung
• 0
0
votes
1
reply
48
views
ERROR; return code from pthread_create() is 22
affy
updated 2 hours ago by
James W. MacDonald
65k • written 2 days ago by
pickingastar
• 0
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 10 days ago by
maria.soler
• 0 • written 16 months ago by
kalavattam
▴ 10
0
votes
0
replies
96
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
20 days ago
Maria Doyle
▴ 70
0
votes
0
replies
95
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
18 days ago
yvonneh
• 0
0
votes
0
replies
9
views
Job:
Post-Doc: Development of a new method to study the distribution of the effect sizes of QTL
StatisticalMethod
Evolution
QuantitativeTrailLocus
Genetics
JobPosting
3 hours ago
pierre.devillemereuil
• 0
0
votes
3
replies
9.2k
views
SingleR Label.Ont
SingleR
updated 9 days ago by
Denis
• 0 • written 8 months ago by
saeed.khalili
• 0
0
votes
4
replies
265
views
Minfi - estimatecellscount
min
minfi
updated 21 days ago by
James W. MacDonald
65k • written 7 weeks ago by
clacarion
• 0
169 results • Page
3 of 4
Recent ...
Replies
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
We have some text about this particular question in the Frequently Asked Questions (FAQ) part of the software vignette.
Answer: How to run allelic imbalance in apeglm
by
Michael Love
42k
You can put 1 / 1 for the ratio when you are missing counts and then set the weight for that matrix cell to 1e-6. Let me know if that's …
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Got you. Thanks again for your comments.
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
Thanks so much for your comment. Yes, this makes sense to me, especially since the effect of the drug is subtle. But it raises a larger con…
Answer: ERROR; return code from pthread_create() is 22
by
James W. MacDonald
65k
Seems OK to me. ``` > dat <- ReadAffy() > dat AffyBatch object size of arrays=744x744 features (20 kb) cdf=HG-U219 (49386 affyids) …
Votes
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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