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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
4 weeks ago • updated 29 days ago
lonn
• 0
0
votes
7
replies
364
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
4 weeks ago • updated 26 days ago
hortense96
• 0
0
votes
0
replies
95
views
News:
Services
flowBeads
4 weeks ago
creativepeptides2018
• 0
0
votes
0
replies
92
views
Enzyme Engineering
BioTIP
4 weeks ago
bocchemistry
• 0
0
votes
0
replies
98
views
News:
TIDES USA 2024
flowBeads
4 weeks ago
bocsci11
• 0
0
votes
0
replies
107
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
4 weeks ago
Maliha Tabassum
• 0
0
votes
4
replies
221
views
flowStats Search Error
flowStats
updated 4 weeks ago by
shepherl
3.9k • written 4 weeks ago by
tholmes
• 0
3
votes
18
replies
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 5 weeks ago by
tian.liu0720
• 0
1
vote
2
replies
172
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
136
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
208
views
Differentially expressed genes in monocle pseudotime
monocle
updated 4 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
kthapa
• 0
4
votes
9
replies
493
views
Memory errors using read.bismark?
dmrseq
bsseq
5 weeks ago • updated 11 days ago
Juan Higareda
• 0
3
votes
3
replies
246
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
5 weeks ago • updated 4 weeks ago
jacques.imbert
• 0
0
votes
1
reply
165
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
230
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
107
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
4 weeks ago
Virangika
• 0
0
votes
0
replies
84
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
4 weeks ago
Henry
▴ 10
1
vote
2
replies
265
views
How to retrieve detailed regression results from deseq2
DESeq2
5 weeks ago • updated 29 days ago
Weiqian
▴ 10
0
votes
4
replies
292
views
DEG with low counts
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 4 weeks ago by
Rajat
• 0
1
vote
2
replies
714
views
GSVA error
GSVA
5 weeks ago • updated 4 weeks ago
Alex
• 0
2
votes
3
replies
345
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 28 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Netanel
• 0
1
vote
3
replies
369
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
148
views
Deseq2 Rlog transformation
DESeq2
updated 4 weeks ago by
ATpoint
★ 4.1k • written 5 weeks ago by
Sahar
• 0
0
votes
2
replies
752
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 3 days ago by
Rosso
• 0 • written 11 months ago by
abhisek001
• 0
1
vote
2
replies
212
views
Design Matrix within group comparison more than two groups
DESeq2
5 weeks ago
hemantcnaik
• 0
2
votes
2
replies
215
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
191
views
[DiffBind] Obtaining normalization factors
DiffBind
5 weeks ago • updated 4 weeks ago
Henry
▴ 10
0
votes
1
reply
151
views
Bioinformatics student
Des
DESeq2
updated 5 weeks ago by
hemantcnaik
• 0 • written 5 weeks ago by
Sahar
• 0
0
votes
0
replies
103
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
5 weeks ago
shepherl
3.9k
2
votes
2
replies
195
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
5 weeks ago • updated 4 weeks ago
daniel.carbajo
• 0
0
votes
3
replies
286
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 4 weeks ago by
W. Evan Johnson
▴ 850 • written 5 weeks ago by
schlumbohm
• 0
5
votes
9
replies
976
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
5 weeks ago • updated 4 weeks ago
Chris
▴ 10
0
votes
0
replies
105
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
5 weeks ago
Stevie Pederson
• 0
2
votes
2
replies
417
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
5 weeks ago
Henry
▴ 10
0
votes
4
replies
242
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
307
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
153
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
5 weeks ago
Eryn
• 0
0
votes
0
replies
97
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
5 weeks ago
Dennis
• 0
0
votes
1
reply
199
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 5 weeks ago by
Guido Hooiveld
★ 4.0k • written 5 weeks ago by
Lucie
• 0
8
votes
23
replies
1.1k
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
247
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
191
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
267
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
462
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 5 weeks ago by
ATpoint
★ 4.1k • written 5 weeks ago by
nhaus
▴ 30
45,670 results • Page
4 of 914
Recent ...
Replies
Answer: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
Your code is poorly readable. Suggest you select and then highlight with markdown using the `10101` button. Generally, colData(dds) must…
Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
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!
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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