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142
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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
22 days ago • updated 14 days ago
glaciya2018
• 0
0
votes
1
reply
98
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 8 days ago by
ATpoint
★ 4.1k • written 8 days ago by
sajadahmad41454
• 0
0
votes
1
reply
165
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 29 days ago by
ATpoint
★ 4.1k • written 4 weeks ago by
quanah.hudson
• 0
0
votes
3
replies
210
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 28 days ago by
Gordon Smyth
50k • written 29 days ago by
prity6459
• 0
0
votes
4
replies
366
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 6 days ago by
Ziliang
• 0 • written 16 days ago by
Ian D.
▴ 70
0
votes
2
replies
166
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
17 days ago • updated 14 days ago
Aurora
• 0
0
votes
5
replies
2.9k
views
DNAString: Standard checksum function?
Biostrings
FASTA
sequencing
8.2 years ago • updated 12 days ago
Henrik Bengtsson
★ 2.4k
0
votes
1
reply
129
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 15 days ago by
4r-rtg
• 0
0
votes
5
replies
324
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 23 days ago by
James W. MacDonald
65k • written 26 days ago by
Gayatri
• 0
0
votes
1
reply
170
views
ATACseq merge peaks
DiffBind
updated 21 days ago by
ATpoint
★ 4.1k • written 23 days ago by
Shloka
• 0
0
votes
1
reply
149
views
covariate with negative and positive values
DESeq2
updated 29 days ago by
Michael Love
42k • written 4 weeks ago by
Brynn
• 0
0
votes
3
replies
151
views
ChAMP installation issue
Cha
ChAMP
4 days ago • updated 3 days ago
e1271094
• 0
0
votes
4
replies
1.2k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 16 hours ago by
angelaesper43
• 0 • written 19 months ago by
Maria Doyle
▴ 70
0
votes
0
replies
93
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
17 days ago
Maria Doyle
▴ 70
0
votes
0
replies
95
views
flowStats for CyTOF
flowStats
15 days ago
tholmes
• 0
0
votes
0
replies
135
views
Empty table plot using plotGseaTable()
fgsea
16 days ago • updated 14 days ago
Chris
▴ 10
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
24 days ago • updated 22 days ago
shuwangxinze1996
• 0
0
votes
1
reply
165
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 23 days ago by
Michael Love
42k • written 23 days ago by
kcarey
• 0
0
votes
0
replies
94
views
Unlocking Potential: NURS FPX Strategies and Insights
levi
NURSFPX
ragene20sttranscriptcluster.db
ssrch
26 days ago
vaxahey107
• 0
0
votes
0
replies
26
views
Minor alleles giving NA from R biomart getBM?
biomaRt
minoralleledata
grch38
getBM
16 hours ago
Jeremy.Clark
• 0
0
votes
3
replies
279
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 29 days ago by
W. Evan Johnson
▴ 850 • written 5 weeks ago by
schlumbohm
• 0
0
votes
1
reply
59
views
Retrieving ceRNA data from the starBase or ENCORI Web API
microRNA
starBase
ceRNA
WebAPI
ENCORI
3 days ago • updated 2 days ago
Bhavya
• 0
0
votes
2
replies
114
views
Batch effect correction: methylome data
sesame
BatchEffect
MethylationArray
updated 3 days ago by
zhouwanding
▴ 10 • written 5 days ago by
Seungmin
• 0
0
votes
0
replies
86
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
11 days ago
Dinesh
• 0
0
votes
3
replies
8.5k
views
SingleR Label.Ont
SingleR
updated 6 days ago by
Denis
• 0 • written 8 months ago by
saeed.khalili
• 0
0
votes
1
reply
135
views
putting my own expression data in deseq2
DESeq2
updated 17 days ago by
ATpoint
★ 4.1k • written 17 days ago by
Dev
• 0
0
votes
0
replies
117
views
dba.plotProfile() plotting and interpretation
DiffBind
14 days ago
Henry
▴ 10
0
votes
0
replies
82
views
News:
Interested in the analysis of Spatial Omics data?
tidySpatialExperiment
SpatialExperiment
MoleculeExperiment
24 days ago
info
▴ 10
0
votes
0
replies
41
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
1 day ago
Shaimaa Gamal
• 0
0
votes
3
replies
68
views
STRINGdb : error with string_db$plot_network()
STRINGdb
updated 9 hours ago by
damian.szk
▴ 80 • written 12 hours ago by
ninidea
• 0
0
votes
0
replies
99
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
23 days ago • updated 18 days ago
Sara
• 0
0
votes
3
replies
219
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 15 days ago by
ATpoint
★ 4.1k • written 16 days ago by
james.zhang20
• 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 7 days ago by
maria.soler
• 0 • written 16 months ago by
kalavattam
▴ 10
0
votes
1
reply
58
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
updated 2 hours ago by
swbarnes2
★ 1.4k • written 15 hours ago by
Ken C
• 0
0
votes
0
replies
13
views
Spam:
Unveiling Unmatched Best Custom Patches
SIMAT
1 day ago
oliverelijhan
0
0
votes
0
replies
42
views
determine k during RUVSeq
RUVSeq
RUVnormalize
1 day ago
Ειρήνη
• 0
0
votes
3
replies
220
views
Couldn't connect to server while using "pathways"
graphite
updated 11 days ago by
Michael Love
42k • written 11 days ago by
fduguchunhui
• 0
0
votes
1
reply
122
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 17 days ago by
shepherl
3.9k • written 17 days ago by
bounlu
• 0
0
votes
2
replies
94
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
1 day ago
makala
• 0
0
votes
3
replies
3.7k
views
[Mfuzz] Error in cmeans(exprs(eset)
Mfuzz
Mfuzz
updated 11 days ago by
Caio
• 0 • written 13.1 years ago by
boczniak767
▴ 720
0
votes
1
reply
138
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 17 days ago by
Michael Love
42k • written 18 days ago by
Agung
• 0
191 results • Page
4 of 4
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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…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network()
by
ninidea
• 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
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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