0
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1
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44
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 7 hours ago by 50k • written 11 hours ago by • 0
0
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1
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49
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Gene-by-sample covariates in limma
Metabolomics limma
updated 7 hours ago by 50k • written 11 hours ago by • 0
0
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1
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134
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
updated 2 hours ago by 50k • written 11 hours ago by ▴ 10
0
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4
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64
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Once again a "Model matrix not full rank"
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9 hours ago • updated 11 minutes ago arfranco ▴ 130
0
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flowStats for CyTOF
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13 hours ago tholmes • 0
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2
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52
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updated 13 hours ago by 41k • written 14 hours ago by • 0
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21
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15 hours ago yvonneh • 0
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15 hours ago Ian D. ▴ 70
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1
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32
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Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 20 hours ago by • 0
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2
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1 day ago • updated 15 hours ago Ian D. ▴ 70
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2
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76
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Deseq2 and Normalization of RNA sequencing data
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1 day ago • updated 7 hours ago kcarey • 0
0
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3
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95
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updated 19 hours ago by ★ 4.1k • written 1 day ago by • 0
0
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1
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103
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Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
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updated 1 day ago by ★ 4.1k • written 1 day ago by • 0
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1 day ago shepherl 3.9k
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Empty table plot using plotGseaTable()
fgsea
1 day ago Chris • 0
0
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3
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116
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Store output of matchPWM()
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updated 1 day ago by 65k • written 1 day ago by ▴ 70
0
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3
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221
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log2FoldChange value is way too different when compared with counts(dds)
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updated 1 day ago by 41k • written 2 days ago by • 0
0
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2
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198
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
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2 days ago • updated 1 day ago Yveto • 0
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6
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SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
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207
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CAMERA limma
2 days ago Chris • 0
1
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1
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84
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 2 days ago by 41k • written 2 days ago by • 0
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1
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76
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Timecourse RNASeq analysis
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0
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1
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87
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 2 days ago by 41k • written 3 days ago by • 0
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46
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News: BioC2024 deadlines approaching
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2 days ago Maria Doyle ▴ 70
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66
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Version 3.15 S4Vectors packages are missing
S4Vectors
updated 2 days ago by 3.9k • written 3 days ago by • 0
0
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1
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88
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putting my own expression data in deseq2
DESeq2
updated 2 days ago by ★ 4.1k • written 2 days ago by • 0
2
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2
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171
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Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
3 days ago Chris • 0
0
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3
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213
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updated 2 days ago by 65k • written 3 days ago by • 0
0
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0
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57
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Could we detect difference at pathway level but not significant different at gene level?
GSVA
3 days ago Chris • 0
3
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3
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199
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
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updated 3 days ago by ★ 4.1k • written 4 days ago by ▴ 10
1
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1
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109
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Dominance Index for Shotgun Metagenomics Data
microbiome
updated 6 days ago by ▴ 40 • written 6 days ago by ★ 1.5k
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PCA plot suggestions
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updated 6 days ago by 41k • written 8 days ago by • 0
1
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3
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190
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 6 days ago by 41k • written 7 days ago by • 0
0
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1
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116
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ATACseq merge peaks
DiffBind
updated 6 days ago by ★ 4.1k • written 8 days ago by • 0
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1
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152
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Improving the design matrices vignette in RNAseq123
RNAseq123
updated 6 days ago by 50k • written 10 days ago by ▴ 730
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7
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297
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7 days ago • updated 6 days ago pl23 • 0
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9
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345
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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updated 7 days ago by 65k • written 7 days ago by • 0
0
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0
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83
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One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools TCGA
7 days ago glaciya2018 • 0
1
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2
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143
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Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
8 days ago • updated 7 days ago ATpoint ★ 4.1k
0
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1
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136
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 8 days ago by 41k • written 8 days ago by • 0
0
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0
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74
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
8 days ago • updated 3 days ago Sara • 0
2
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5
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241
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get BM error
ensembldb
updated 8 days ago by 65k • written 8 days ago by • 0
2
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5
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216
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How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 7 days ago by 65k • written 9 days ago by • 0
0
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Exon-exon Junction Analysis for Variable-length Exons
Rsubread
8 days ago Dario Strbenac ★ 1.5k
1
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3
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203
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DESeq2
updated 8 days ago by 41k • written 8 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
8 days ago • updated 7 days ago winwater0928 • 0
3
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1
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299
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 9 days ago by 41k • written 9 days ago by ▴ 40
1
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1
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162
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Citation for edgeR user guide
edgeR
updated 9 days ago by 50k • written 9 days ago by ▴ 30
0
votes
7
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688
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News: List of Deprecated Packages for Bioc3.19
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9 weeks ago • updated 9 days ago shepherl 3.9k
45,611 results • Page 1 of 913
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Replies
Comment: Once again a "Model matrix not full rank" by arfranco ▴ 130
But.. How to run a temporal assay?
Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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