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0
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0
replies
104
views
flowStats for CyTOF
flowStats
24 days ago
tholmes
• 0
0
votes
1
reply
154
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 24 days ago by
4r-rtg
• 0
0
votes
4
replies
274
views
Minfi - estimatecellscount
min
minfi
updated 27 days ago by
James W. MacDonald
66k • written 8 weeks ago by
clacarion
• 0
0
votes
7
replies
363
views
ChAMP installation issue
Cha
ChAMP
updated 4 days ago by
James W. MacDonald
66k • written 13 days ago by
e1271094
• 0
0
votes
0
replies
84
views
Treeio as.treedata function seq lenght error
treeio
18 days ago
nromerov
• 0
0
votes
5
replies
421
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
25 days ago • updated 2 days ago
Ian D.
▴ 70
0
votes
0
replies
44
views
Processing of curatedmetagenomics
curatedMetagenomicData
6 days ago
Edward
• 0
0
votes
0
replies
145
views
Empty table plot using plotGseaTable()
fgsea
25 days ago • updated 22 days ago
Chris
▴ 10
0
votes
0
replies
42
views
News:
Bioconductor Build System
Builds
Bioconductor
2 days ago
shepherl
3.9k
0
votes
0
replies
64
views
Difference in Contrast in DiffBind
DiffBind
11 days ago
zzrammal
• 0
0
votes
0
replies
100
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
10 days ago
Anton01
• 0
0
votes
0
replies
106
views
need help with Diffbind multiple groups
DiffBind
ChIPSeqData
19 days ago
Dinesh
• 0
0
votes
44
replies
3.2k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges
nullranges
updated 12 days ago by
Michael Love
42k • written 15 months ago by
Poonam
• 0
0
votes
1
reply
124
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 17 days ago by
ATpoint
★ 4.2k • written 17 days ago by
sajadahmad41454
• 0
0
votes
0
replies
105
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
4 weeks ago • updated 27 days ago
Sara
• 0
0
votes
0
replies
41
views
Conditional analysis
GENESIS
5 days ago
SuperDad
• 0
0
votes
3
replies
117
views
pathview error
KEGGgraph
KEGG
updated 3 days ago by
Guido Hooiveld
★ 4.0k • written 4 days ago by
Fara
• 0
0
votes
1
reply
144
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 26 days ago by
Michael Love
42k • written 26 days ago by
Agung
• 0
0
votes
1
reply
125
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 12 days ago by
Michael Love
42k • written 13 days ago by
piemmea
• 0
0
votes
0
replies
13
views
Error in render R qmd document (could not find function "process")
quantro
3 hours ago
Chutian
• 0
0
votes
4
replies
1.3k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 9 days ago by
angelaesper43
• 0 • written 19 months ago by
Maria Doyle
▴ 70
0
votes
2
replies
764
views
Help with ENmix readidat
ENmix
IlluminaHumanMethylationEPICmanifest
updated 5 days ago by
James W. MacDonald
66k • written 2.0 years ago by
Daphna
• 0
0
votes
1
reply
1.4k
views
DSS CpG coverage threshold
DSS
WGBS
coverage
updated 17 days ago by
j.gilbert
• 0 • written 6.6 years ago by
floriandeckert
▴ 30
0
votes
3
replies
163
views
Assymetric MA plot with no overall trend
DESeq2
DifferentialExpression
updated 11 days ago by
Michael Love
42k • written 11 days ago by
Kasper
• 0
0
votes
5
replies
197
views
all variables in design formula must be columns in colData (Deseq2) error
BatchQC
batchinDeseq2.
columnsincolData.
7 days ago • updated 6 days ago
Galina
• 0
0
votes
0
replies
29
views
conumee with Infinium MethylationEPIC v2.0
conumee
1 day ago
Maximus
• 0
0
votes
0
replies
94
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
24 days ago
Ian D.
▴ 70
0
votes
6
replies
620
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
9 days ago • updated 6 days ago
Ken C
• 0
0
votes
0
replies
67
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
10 days ago
k200987
• 0
0
votes
0
replies
74
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
10 days ago
danalvoronov
▴ 10
0
votes
3
replies
311
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 24 days ago by
Michael Love
42k • written 25 days ago by
HAK
• 0
0
votes
0
replies
93
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer
ShinyApps
16 days ago
neilzhao
▴ 30
0
votes
0
replies
12
views
Spam:
Understanding Laser Hair Removal?
healthyControlsPresenceChecker
6 days ago
shahrozimmac
0
0
votes
0
replies
152
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 23 days ago
glaciya2018
• 0
0
votes
5
replies
2.9k
views
DNAString: Standard checksum function?
Biostrings
FASTA
sequencing
8.2 years ago • updated 20 days ago
Henrik Bengtsson
★ 2.4k
0
votes
1
reply
735
views
How to arrange multiple plots into one page in NOISeq?
noiseq
RNA-seq
quality control
updated 5 days ago by
baptiste.bidon
• 0 • written 4.8 years ago by
ag1805x
▴ 80
0
votes
0
replies
81
views
ReactomeGSA for RNASeq
ReactomeGSA
BatchEffect
RNASeqData
10 days ago
Shaimaa Gamal
• 0
0
votes
6
replies
320
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 22 days ago by
swbarnes2
★ 1.4k • written 23 days ago by
arfranco
▴ 130
0
votes
4
replies
241
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq
Rsubread
updated 2 days ago by
Wei Shi
★ 3.6k • written 3 days ago by
atan
• 0
0
votes
1
reply
202
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 13 days ago by
Guido Hooiveld
★ 4.0k • written 14 days ago by
aogunbaw
• 0
0
votes
2
replies
202
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 4 weeks ago by
taur.vil
• 0
0
votes
2
replies
134
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
13 days ago • updated 12 days ago
Yveto
• 0
0
votes
0
replies
50
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq
scRNAseq
7 days ago
Bibi
• 0
0
votes
1
reply
202
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 16 days ago by
ATpoint
★ 4.2k • written 16 days ago by
sajadahmad41454
• 0
0
votes
2
replies
222
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
24 days ago • updated 23 days ago
kcarey
• 0
0
votes
4
replies
167
views
Volcano plot of scRNA-seq data not "centered"
DESeq2
updated 9 hours ago by
ATpoint
★ 4.2k • written 2 days ago by
tjl
• 0
0
votes
3
replies
2.1k
views
maSigPro genes from clusters
masigpro
clustering
updated 9 days ago by
anne-laure
• 0 • written 7.9 years ago by
ls299
• 0
0
votes
0
replies
20
views
How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat
DESeq2
single-cell
scRNA
Pseudobulk
9 hours ago
Sara
• 0
0
votes
0
replies
24
views
News:
Legacy Bioconductor Installation
Installation
Bioconductor
2 days ago
shepherl
3.9k
0
votes
2
replies
187
views
DESeq2 v1.35.0
DESeq2
updated 24 days ago by
Michael Love
42k • written 24 days ago by
Espresso
• 0
174 results • Page
3 of 4
Recent ...
Replies
Comment: Volcano plot of scRNA-seq data not "centered"
by
ATpoint
★ 4.2k
My comment was generic. If your experiment causes drastic shifts then the situation might be different. The advise is the same: Try to use …
Comment: conumee with Infinium MethylationEPIC v2.0
by
Maximus
• 0
Hi Sole, If there is a combined mixture of MSet of 450K, EPIC and EPICv2, how should I create an annotation object? I tried to create anno…
Comment: Volcano plot of scRNA-seq data not "centered"
by
tjl
• 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora
by
James W. MacDonald
66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Comment: Cannot install oligo on Fedora
by
James W. MacDonald
66k
There is the `zlibbioc` package that provides the headers for zlib 1.2.5, that I think you should be able to use, although that would requi…
Votes
A: Analyzing data without replicates using DiffBind
A: Analyzing data without replicates using DiffBind
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
DESeq2 swap ensembl gene id rownames with gene symbol column
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
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