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91
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Enzyme Engineering
BioTIP
4 weeks ago
bocchemistry
• 0
0
votes
0
replies
96
views
News:
TIDES USA 2024
flowBeads
4 weeks ago
bocsci11
• 0
0
votes
0
replies
105
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
4 weeks ago
Maliha Tabassum
• 0
0
votes
4
replies
218
views
flowStats Search Error
flowStats
updated 4 weeks ago by
shepherl
3.9k • written 4 weeks ago by
tholmes
• 0
3
votes
18
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3.0k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 4 weeks ago
shepherl
3.9k
0
votes
1
reply
152
views
SNP locus package for mouse?
SNPlocs
packFinder
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
tian.liu0720
• 0
1
vote
2
replies
171
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
4 weeks ago
Ana
• 0
0
votes
5
replies
1.7k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 13 months ago by
mauricio.microbiol
• 0
0
votes
1
reply
135
views
what is the sampleFiles
chipseq
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
zhulin
• 0
1
vote
1
reply
207
views
Differentially expressed genes in monocle pseudotime
monocle
updated 4 weeks ago by
Gordon Smyth
50k • written 4 weeks ago by
kthapa
• 0
4
votes
9
replies
489
views
Memory errors using read.bismark?
dmrseq
bsseq
5 weeks ago • updated 10 days ago
Juan Higareda
• 0
3
votes
3
replies
244
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
5 weeks ago • updated 29 days ago
jacques.imbert
• 0
0
votes
1
reply
164
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 4 weeks ago by
kamryncole1963
• 0 • written 5 weeks ago by
Sara
• 0
0
votes
3
replies
229
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 4 weeks ago by
andrebolerbarros
▴ 20
0
votes
0
replies
105
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
4 weeks ago
Virangika
• 0
0
votes
0
replies
82
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
4 weeks ago
Henry
▴ 10
1
vote
2
replies
262
views
How to retrieve detailed regression results from deseq2
DESeq2
5 weeks ago • updated 28 days ago
Weiqian
▴ 10
0
votes
4
replies
291
views
DEG with low counts
DESeq2
updated 28 days ago by
Michael Love
42k • written 4 weeks ago by
Rajat
• 0
1
vote
2
replies
702
views
GSVA error
GSVA
4 weeks ago
Alex
• 0
2
votes
3
replies
344
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
4 weeks ago
daniel.carbajo
• 0
3
votes
3
replies
368
views
permutation test in edgeR
rna-seq
edgeR
updated 27 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Netanel
• 0
1
vote
3
replies
368
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 4 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Simran
• 0
0
votes
1
reply
144
views
Deseq2 Rlog transformation
DESeq2
updated 4 weeks ago by
ATpoint
★ 4.1k • written 4 weeks ago by
Sahar
• 0
0
votes
2
replies
748
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 2 days ago by
Rosso
• 0 • written 11 months ago by
abhisek001
• 0
1
vote
2
replies
211
views
Design Matrix within group comparison more than two groups
DESeq2
5 weeks ago • updated 4 weeks ago
hemantcnaik
• 0
2
votes
2
replies
213
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
5 weeks ago
julia_mcdonough
• 0
2
votes
2
replies
190
views
[DiffBind] Obtaining normalization factors
DiffBind
5 weeks ago • updated 4 weeks ago
Henry
▴ 10
0
votes
1
reply
149
views
Bioinformatics student
Des
DESeq2
updated 5 weeks ago by
hemantcnaik
• 0 • written 5 weeks ago by
Sahar
• 0
0
votes
0
replies
101
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
5 weeks ago
shepherl
3.9k
2
votes
2
replies
191
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
5 weeks ago • updated 4 weeks ago
daniel.carbajo
• 0
0
votes
3
replies
280
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
5
votes
9
replies
974
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
5 weeks ago • updated 29 days ago
Chris
▴ 10
0
votes
0
replies
103
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
5 weeks ago
Stevie Pederson
• 0
2
votes
2
replies
416
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
5 weeks ago
Henry
▴ 10
0
votes
4
replies
241
views
Storing directories inside an ExperimentHub package?
ExperimentHub
5 weeks ago
Tim Barry
• 0
0
votes
0
replies
117
views
News:
Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing
Sequencing
SequencingData
5 weeks ago
communication
• 0
3
votes
6
replies
305
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
5 weeks ago
nhaus
▴ 30
0
votes
1
reply
196
views
DESeq2 gives an error and R crashes
DESeq2
5 weeks ago
Shefali
• 0
0
votes
0
replies
151
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
5 weeks ago
Eryn
• 0
0
votes
0
replies
96
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
5 weeks ago
Dennis
• 0
0
votes
1
reply
197
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 4 weeks ago by
Guido Hooiveld
★ 4.0k • written 5 weeks ago by
Lucie
• 0
8
votes
23
replies
1.0k
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 5 weeks ago by
Robert Castelo
★ 3.3k • written 5 weeks ago by
Bine
▴ 40
0
votes
1
reply
154
views
Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 5 weeks ago by
ATpoint
★ 4.1k • written 5 weeks ago by
Merav
• 0
0
votes
2
replies
245
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 5 weeks ago by
Michael Love
42k • written 6 weeks ago by
nhaus
▴ 30
0
votes
1
reply
187
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 5 weeks ago by
Michael Love
42k • written 5 weeks ago by
Adelaide
• 0
0
votes
2
replies
265
views
Regressing out batch effects
DESeq2
updated 5 weeks ago by
Michael Love
42k • written 6 weeks ago by
kys91240
• 0
5
votes
6
replies
456
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 4 weeks ago by
ATpoint
★ 4.1k • written 5 weeks ago by
nhaus
▴ 30
0
votes
1
reply
162
views
BAM write error in HTSeqGenie
HTSeqGenie
BAM
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
zh9118
• 0
1
vote
6
replies
522
views
GSVA on separate healthy and disease datasets
GSVA
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
Lucy
▴ 60
0
votes
0
replies
128
views
ggtree tip label position (depth)
ggtree
5 weeks ago
Roope
• 0
1,738 results • Page
4 of 35
Recent ...
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Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
JKim
• 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
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" …
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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