3
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1
reply
147
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How to save the DEXSeq results
DEXSeq
updated 11 days ago by 42k • written 11 days ago by • 0
4
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5
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316
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Method to find pathways different between 2 groups
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12 days ago • updated 2 days ago Chris ▴ 10
0
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3
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220
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Couldn't connect to server while using "pathways"
graphite
updated 11 days ago by 42k • written 11 days ago by • 0
2
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1
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141
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Trim/Filter out-of-bounds GRanges
GenomicRanges
updated 11 days ago by 42k • written 11 days ago by ▴ 70
1
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1
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185
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Handling multiple differential expression comparisons
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updated 12 days ago by 42k • written 14 days ago by ▴ 10
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2
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224
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fgsea significant result
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13 days ago • updated 12 days ago Chris ▴ 10
0
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44
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3.1k
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How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges nullranges
updated 3 days ago by 42k • written 15 months ago by • 0
0
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6
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290
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Once again a "Model matrix not full rank"
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updated 13 days ago by ★ 1.4k • written 15 days ago by ▴ 130
1
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2
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397
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 14 days ago by 50k • written 14 days ago by • 0
2
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3
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262
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package goseq seems to be not available on the latest version of R
goseq
updated 11 days ago by 50k • written 14 days ago by ▴ 20
2
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3
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254
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 12 days ago by ★ 4.1k • written 14 days ago by • 0
0
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0
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117
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dba.plotProfile() plotting and interpretation
DiffBind
14 days ago Henry ▴ 10
0
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1
reply
172
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 15 days ago by 50k • written 15 days ago by • 0
0
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1
reply
154
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Gene-by-sample covariates in limma
Metabolomics limma
updated 15 days ago by 50k • written 15 days ago by • 0
4
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2
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619
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
15 days ago • updated 11 days ago gene_bioconductor ▴ 10
0
votes
0
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96
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flowStats for CyTOF
flowStats
15 days ago tholmes • 0
0
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2
replies
159
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DESeq2 v1.35.0
DESeq2
updated 15 days ago by 42k • written 15 days ago by • 0
0
votes
0
replies
89
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
15 days ago yvonneh • 0
0
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0
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83
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How to create consensus peak sets for each group to use in DiffBind?
DiffBind
15 days ago Ian D. ▴ 70
0
votes
1
reply
129
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Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 15 days ago by • 0
0
votes
4
replies
367
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More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 6 days ago by • 0 • written 16 days ago by ▴ 70
0
votes
2
replies
209
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Deseq2 and Normalization of RNA sequencing data
DESeq2
16 days ago • updated 15 days ago kcarey • 0
0
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3
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219
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Differences in differential analysis methods for RNA-Seq
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updated 15 days ago by ★ 4.1k • written 16 days ago by • 0
1
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3
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303
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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 9 days ago by ★ 4.1k • written 16 days ago by • 0
4
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0
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135
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News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
16 days ago shepherl 3.9k
0
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0
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135
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Empty table plot using plotGseaTable()
fgsea
16 days ago • updated 14 days ago Chris ▴ 10
0
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3
replies
300
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 16 days ago by 42k • written 17 days ago by • 0
1
vote
2
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288
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
17 days ago • updated 16 days ago Yveto • 0
0
votes
1
reply
262
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How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 17 days ago by 65k • written 18 days ago by • 0
3
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4
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260
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Help with error using camera() in limma
CAMERA limma
17 days ago Chris ▴ 10
1
vote
1
reply
155
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 17 days ago by 42k • written 17 days ago by • 0
0
votes
2
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166
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Timecourse RNASeq analysis
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17 days ago • updated 14 days ago Aurora • 0
0
votes
1
reply
138
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 17 days ago by 42k • written 18 days ago by • 0
0
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0
replies
93
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News: BioC2024 deadlines approaching
BioC2024 Bioconductor Community
17 days ago Maria Doyle ▴ 70
0
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1
reply
122
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Version 3.15 S4Vectors packages are missing
S4Vectors
updated 17 days ago by 3.9k • written 18 days ago by • 0
0
votes
1
reply
135
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putting my own expression data in deseq2
DESeq2
updated 17 days ago by ★ 4.1k • written 17 days ago by • 0
2
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2
replies
234
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Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
18 days ago Chris ▴ 10
0
votes
3
replies
273
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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 17 days ago by 65k • written 18 days ago by • 0
0
votes
0
replies
94
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Could we detect difference at pathway level but not significant different at gene level?
GSVA
18 days ago Chris ▴ 10
3
votes
3
replies
268
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 18 days ago by ★ 4.1k • written 19 days ago by ▴ 10
1
vote
1
reply
152
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 21 days ago by ▴ 40 • written 21 days ago by ★ 1.5k
0
votes
2
replies
226
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PCA plot suggestions
DESeq2 PCAtools
updated 21 days ago by 42k • written 23 days ago by • 0
1
vote
3
replies
253
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 21 days ago by 42k • written 22 days ago by • 0
0
votes
1
reply
170
views
ATACseq merge peaks
DiffBind
updated 21 days ago by ★ 4.1k • written 23 days ago by • 0
1
vote
2
replies
211
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Improving the design matrices vignette in RNAseq123
RNAseq123
25 days ago • updated 11 days ago Lluís Revilla Sancho ▴ 730
1
vote
7
replies
357
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Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
22 days ago • updated 21 days ago pl23 • 0
2
votes
9
replies
426
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 22 days ago by 65k • written 22 days ago by • 0
0
votes
0
replies
142
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools TCGA
22 days ago • updated 14 days ago glaciya2018 • 0
1
vote
2
replies
175
views
Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
23 days ago • updated 22 days ago ATpoint ★ 4.1k
0
votes
1
reply
165
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 23 days ago by 42k • written 23 days ago by • 0
191 results • Page 2 of 4
Recent ...
Replies
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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