0
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1
reply
169
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 12 days ago by 50k • written 13 days ago by • 0
0
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1
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152
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Gene-by-sample covariates in limma
Metabolomics limma
updated 12 days ago by 50k • written 13 days ago by • 0
4
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2
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613
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
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13 days ago • updated 9 days ago gene_bioconductor ▴ 10
0
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95
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flowStats for CyTOF
flowStats
13 days ago tholmes • 0
0
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2
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156
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DESeq2 v1.35.0
DESeq2
updated 13 days ago by 42k • written 13 days ago by • 0
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0
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88
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
13 days ago yvonneh • 0
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0
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79
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How to create consensus peak sets for each group to use in DiffBind?
DiffBind
13 days ago Ian D. ▴ 70
0
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1
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124
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Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 13 days ago by • 0
0
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4
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350
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More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 3 days ago by • 0 • written 14 days ago by ▴ 70
0
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2
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202
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Deseq2 and Normalization of RNA sequencing data
DESeq2
13 days ago • updated 12 days ago kcarey • 0
0
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3
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204
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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
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3
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294
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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
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0
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127
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News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
14 days ago shepherl 3.9k
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0
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129
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Empty table plot using plotGseaTable()
fgsea
14 days ago • updated 11 days ago Chris ▴ 10
0
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3
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294
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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
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2
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279
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
14 days ago • updated 13 days ago Yveto • 0
0
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1
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259
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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
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4
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256
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Help with error using camera() in limma
CAMERA limma
15 days ago Chris ▴ 10
1
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1
reply
146
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 15 days ago by 42k • written 15 days ago by • 0
0
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2
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161
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Timecourse RNASeq analysis
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15 days ago • updated 12 days ago Aurora • 0
0
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1
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135
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 15 days ago by 42k • written 16 days ago by • 0
0
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0
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91
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News: BioC2024 deadlines approaching
BioC2024 Bioconductor Community
15 days ago Maria Doyle ▴ 70
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1
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117
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Version 3.15 S4Vectors packages are missing
S4Vectors
updated 15 days ago by 3.9k • written 15 days ago by • 0
0
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1
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131
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putting my own expression data in deseq2
DESeq2
updated 15 days ago by ★ 4.1k • written 15 days ago by • 0
2
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2
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227
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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 Chris ▴ 10
0
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3
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269
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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
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0
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90
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Could we detect difference at pathway level but not significant different at gene level?
GSVA
16 days ago Chris ▴ 10
3
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3
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259
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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
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1
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148
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Dominance Index for Shotgun Metagenomics Data
microbiome
updated 18 days ago by ▴ 40 • written 19 days ago by ★ 1.5k
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2
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224
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PCA plot suggestions
DESeq2 PCAtools
updated 19 days ago by 42k • written 20 days ago by • 0
1
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3
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248
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Deseq2. decontXcounts not integers. Useful alternative?
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updated 19 days ago by 42k • written 20 days ago by • 0
0
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1
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164
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ATACseq merge peaks
DiffBind
updated 19 days ago by ★ 4.1k • written 21 days ago by • 0
1
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2
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Improving the design matrices vignette in RNAseq123
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23 days ago • updated 9 days ago Lluís Revilla Sancho ▴ 730
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Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
20 days ago • updated 19 days ago pl23 • 0
2
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9
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 20 days ago by 65k • written 20 days ago by • 0
0
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0
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139
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One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
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20 days ago • updated 12 days ago glaciya2018 • 0
1
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2
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172
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21 days ago • updated 20 days ago ATpoint ★ 4.1k
0
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1
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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
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98
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
21 days ago • updated 16 days ago Sara • 0
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get BM error
ensembldb
updated 21 days ago by 65k • written 21 days ago by • 0
2
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5
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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
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Exon-exon Junction Analysis for Variable-length Exons
Rsubread
21 days ago Dario Strbenac ★ 1.5k
1
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3
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updated 21 days ago by 42k • written 21 days ago by ▴ 20
1
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4
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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
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325
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DESeq2
updated 21 days ago by 42k • written 22 days ago by ▴ 40
1
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2
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Citation for edgeR user guide
edgeR
written 22 days ago by ▴ 30
0
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7
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738
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News: List of Deprecated Packages for Bioc3.19
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10 weeks ago • updated 22 days ago shepherl 3.9k
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128
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Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 22 days ago by 65k • written 22 days ago by ▴ 10
0
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8
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377
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DESeq2 output used for PCA plot on R studio
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updated 20 days ago by ★ 1.4k • written 22 days ago by • 0
0
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0
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tidySpatialExperiment SpatialExperiment MoleculeExperiment
22 days ago info ▴ 10
1,000 results • Page 2 of 20
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Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Marcel Ramos 690
`BiocManager` does not install local packages. It only installs Bioconductor, CRAN, and GitHub ones. You should install local packages w…
Comment: error running enricher from clusterprofiler by Yael • 0
It worked!!! Thanks alot, i think something in the gene_list wasnt right... Thanks agian
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`. …
Votes
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Answer: Trim/Filter out-of-bounds GRanges
Comment: How to correctly adjust for gender in edgeR
Create protein sequences including variants from a VCF file
A: DEXSeq design formula
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