0
votes
1
reply
169
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 12 days ago by 50k • written 13 days ago by • 0
0
votes
1
reply
151
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 12 days ago by 50k • written 13 days ago by • 0
4
votes
2
replies
613
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
12 days ago • updated 9 days ago gene_bioconductor ▴ 10
0
votes
0
replies
95
views
flowStats for CyTOF
flowStats
13 days ago tholmes • 0
0
votes
2
replies
156
views
DESeq2 v1.35.0
DESeq2
updated 13 days ago by 42k • written 13 days ago by • 0
0
votes
0
replies
88
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
13 days ago yvonneh • 0
0
votes
0
replies
79
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
13 days ago Ian D. ▴ 70
0
votes
1
reply
124
views
Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 13 days ago by • 0
0
votes
4
replies
347
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 3 days ago by • 0 • written 14 days ago by ▴ 70
0
votes
2
replies
201
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
13 days ago • updated 12 days ago kcarey • 0
0
votes
3
replies
204
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 13 days ago by ★ 4.1k • written 13 days ago by • 0
1
vote
3
replies
293
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 7 days ago by ★ 4.1k • written 13 days ago by • 0
4
votes
0
replies
125
views
News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
13 days ago shepherl 3.9k
0
votes
0
replies
129
views
Empty table plot using plotGseaTable()
fgsea
14 days ago • updated 11 days ago Chris ▴ 10
0
votes
3
replies
293
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 13 days ago by 42k • written 14 days ago by • 0
1
vote
2
replies
276
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
14 days ago • updated 13 days ago Yveto • 0
0
votes
1
reply
259
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 15 days ago by 65k • written 15 days ago by • 0
3
votes
4
replies
256
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Help with error using camera() in limma
CAMERA limma
15 days ago • updated 14 days ago Chris ▴ 10
1
vote
1
reply
146
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 15 days ago by 42k • written 15 days ago by • 0
0
votes
2
replies
161
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
15 days ago • updated 12 days ago Aurora • 0
0
votes
1
reply
135
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 15 days ago by 42k • written 15 days ago by • 0
0
votes
0
replies
91
views
News: BioC2024 deadlines approaching
BioC2024 Bioconductor Community
15 days ago Maria Doyle ▴ 70
0
votes
1
reply
117
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 15 days ago by 3.9k • written 15 days ago by • 0
0
votes
1
reply
131
views
putting my own expression data in deseq2
DESeq2
updated 15 days ago by ★ 4.1k • written 15 days ago by • 0
2
votes
2
replies
226
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Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
16 days ago • updated 15 days ago Chris ▴ 10
0
votes
3
replies
269
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 15 days ago by 65k • written 16 days ago by • 0
0
votes
0
replies
90
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
16 days ago Chris ▴ 10
3
votes
3
replies
259
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 16 days ago by ★ 4.1k • written 16 days ago by ▴ 10
1
vote
1
reply
148
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 18 days ago by ▴ 40 • written 19 days ago by ★ 1.5k
0
votes
2
replies
224
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PCA plot suggestions
DESeq2 PCAtools
updated 19 days ago by 42k • written 20 days ago by • 0
1
vote
3
replies
248
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 19 days ago by 42k • written 19 days ago by • 0
0
votes
1
reply
164
views
ATACseq merge peaks
DiffBind
updated 19 days ago by ★ 4.1k • written 21 days ago by • 0
1
vote
2
replies
209
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Improving the design matrices vignette in RNAseq123
RNAseq123
23 days ago • updated 9 days ago Lluís Revilla Sancho ▴ 730
1
vote
7
replies
346
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Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
20 days ago • updated 19 days ago pl23 • 0
2
votes
9
replies
420
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 19 days ago by 65k • written 20 days ago by • 0
0
votes
0
replies
139
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools TCGA
20 days ago • updated 12 days ago glaciya2018 • 0
1
vote
2
replies
172
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Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
21 days ago • updated 20 days ago ATpoint ★ 4.1k
0
votes
1
reply
164
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 20 days ago by 42k • written 21 days ago by • 0
0
votes
0
replies
98
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
21 days ago • updated 16 days ago Sara • 0
2
votes
5
replies
298
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get BM error
ensembldb
updated 21 days ago by 65k • written 21 days ago by • 0
2
votes
5
replies
255
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How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 20 days ago by 65k • written 21 days ago by • 0
0
votes
0
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96
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Exon-exon Junction Analysis for Variable-length Exons
Rsubread
21 days ago Dario Strbenac ★ 1.5k
1
vote
3
replies
231
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Different Shrunk Log2FC according with reference
DESeq2
updated 21 days ago by 42k • written 21 days ago by ▴ 20
1
vote
4
replies
352
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
21 days ago • updated 19 days ago winwater0928 • 0
3
votes
1
reply
325
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 21 days ago by 42k • written 22 days ago by ▴ 40
1
vote
2
replies
200
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Citation for edgeR user guide
edgeR
written 21 days ago by ▴ 30
0
votes
7
replies
738
views
News: List of Deprecated Packages for Bioc3.19
Release Devel ExperimentData Software
10 weeks ago • updated 22 days ago shepherl 3.9k
1
vote
1
reply
128
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 22 days ago by 65k • written 22 days ago by ▴ 10
0
votes
8
replies
376
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 20 days ago by ★ 1.4k • written 22 days ago by • 0
0
votes
0
replies
79
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News: Interested in the analysis of Spatial Omics data?
tidySpatialExperiment SpatialExperiment MoleculeExperiment
22 days ago info ▴ 10
45,655 results • Page 2 of 914
Recent ...
Replies
Comment: Create protein sequences including variants from a VCF file by Yun • 0
This cannot work for a SNV file, since `injectSNPs` need a `SNPlocs` object
Comment: Can log2cpm be used for proteomics data normalization? by Daniel • 0
Thank you for the quick reply and I apologize for it being on the wrong thread but the "post tag" function wasn't working properly.
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
I have arranged the code again following the other post and also the script you suggested. Now, I managed to install `org.Vdahliae.eg.db`. …
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
Thanks again Guido, I will try to run the script you have suggested and see if I can install the package. Yes, I have seen this message a…
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Guido Hooiveld ★ 4.0k
FWIW: based on [previous posts][1] it is suggested to install like this: install.packages(pkgs="./org.Vdahliae.eg.db", repos=NULL, typ…
Votes
Comment: How to correctly adjust for gender in edgeR
Create protein sequences including variants from a VCF file
A: DEXSeq design formula
Answer: SGSeq: moving toward diffex from SGSeq analysis
Answer: How to design DEXSeq formula for multiple variables
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