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445
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updated 29 days ago by ★ 4.1k • written 4 weeks ago by ▴ 30
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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updated 17 days ago by 65k • written 17 days ago by • 0
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limma Intercept vs No-intercept models completely changing DMR results?
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updated 17 days ago by ★ 1.4k • written 19 days ago by • 0
3
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permutation test in edgeR
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updated 21 days ago by 50k • written 4 weeks ago by • 0
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Why is my gene not significantly differentially expressed?
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updated 27 days ago by 50k • written 4 weeks ago by • 0
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4
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Opposite sign of LFC in count plots of DEGs (DESeq2)
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18 days ago • updated 16 days ago winwater0928 • 0
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Math expression in shapeCustom legend in EnhancedVolcano
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17 days ago • updated 16 days ago pl23 • 0
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CombineArrays for EPIC and EPIC V2
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5 weeks ago • updated 9 days ago Kim • 0
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27 days ago • updated 26 days ago daniel.carbajo • 0
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Methylation Analysis experiment design using Limma
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25 days ago • updated 19 days ago hortense96 • 0
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
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updated 18 days ago by 42k • written 19 days ago by ▴ 40
1
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23 days ago BioinfGuru ▴ 30
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Error for AnnotationForge makeOrgPackageFromNCBI function
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updated 18 days ago by 65k • written 21 days ago by • 0
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More regions in union when increasing DBA$config$mergeOverlap
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get BM error
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updated 18 days ago by 65k • written 18 days ago by • 0
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updated 2 days ago by 50k • written 24 days ago by • 0
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4
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DEG with low counts
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updated 23 days ago by 42k • written 28 days ago by • 0
1
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3
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log2FoldChange value is way too different when compared with counts(dds)
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updated 11 days ago by 42k • written 12 days ago by • 0
2
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7
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272
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deseq2 results
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4 days ago • updated 1 day ago sajadahmad41454 • 0
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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 4 days ago by ★ 4.1k • written 11 days ago by • 0
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3
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270
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A ComBat-seq issue: the covariates are confounded
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updated 24 days ago by ▴ 850 • written 4 weeks ago by • 0
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Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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6 weeks ago • updated 23 days ago isaac.vock • 0
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
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11 days ago • updated 10 days ago Yveto • 0
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3
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260
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updated 12 days ago by 65k • written 13 days ago by • 0
0
votes
2
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featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
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19 days ago • updated 17 days ago shuwangxinze1996 • 0
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updated 13 days ago by 65k • written 6 weeks ago by • 0
1
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4
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Error EPICv2 ChAMP
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updated 20 days ago by 65k • written 24 days ago by • 0
3
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
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updated 13 days ago by ★ 4.1k • written 13 days ago by ▴ 10
0
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6
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253
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Once again a "Model matrix not full rank"
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2
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updated 17 days ago by 65k • written 19 days ago by • 0
1
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2
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250
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How to retrieve detailed regression results from deseq2
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4 weeks ago • updated 23 days ago Weiqian ▴ 10
0
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reply
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How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
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updated 12 days ago by 65k • written 12 days ago by • 0
3
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4
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Method to find pathways different between 2 groups
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updated 5 days ago by 50k • written 6 days ago by • 0
0
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4
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248
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Differential peaks that were not identified in diffbind were identified in diseq2
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25 days ago • updated 22 days ago lonn • 0
3
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Help with error using camera() in limma
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12 days ago Chris • 0
1
vote
3
replies
238
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Deseq2. decontXcounts not integers. Useful alternative?
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updated 16 days ago by 42k • written 17 days ago by • 0
3
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5
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234
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Help with running egsea()
EGSEA
6 days ago • updated 4 days ago Chris • 0
3
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3
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DESeq2 - dispersion estimation when there is none
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updated 19 days ago by 42k • written 20 days ago by • 0
1
vote
2
replies
228
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significant difference of p-values with dream() after updating VariancePartition
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24 days ago Le • 0
1
vote
3
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226
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Different Shrunk Log2FC according with reference
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updated 18 days ago by 42k • written 18 days ago by ▴ 20
3
votes
3
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225
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Reading huge bismark coverage files using bbseq::read.bismark
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4 weeks ago • updated 24 days ago jacques.imbert • 0
0
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224
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RNAseq:Technical replicates from different batches
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23 days ago • updated 20 days ago catv • 0
3
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2
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Cannabis and KEGGgraph
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updated 20 days ago by ★ 3.9k • written 23 days ago by ▴ 10
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votes
2
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219
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PCA plot suggestions
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updated 16 days ago by 42k • written 17 days ago by • 0
2
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3
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Too many significant genes when integrating gtex and tcga
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updated 7 days ago by ★ 4.1k • written 9 days ago by • 0
2
votes
2
replies
216
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Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
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13 days ago Chris • 0
188 results • Page 2 of 4
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Comment: More regions in union when increasing DBA$config$mergeOverlap by Ziliang • 0
I am so confused and frustrated learning to use this software. Isn't how you merge the peaksets one of the most important steps for the com…
Answer: SingleR Label.Ont by Denis • 0
[Jackpot City Casino][1] is the perfect option when looking for an online casino in Canada for an exciting vacation and huge winnings that …
Comment: deseq2 results by sajadahmad41454 • 0
thank you so much and sorry for bothering you again and again, it is urgent because it is my project deadline. i have removed that sample a…
Comment: deseq2 results by swbarnes2 ★ 1.4k
Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
Comment: Can't post a question containing code? by NATASHA • 0
did you find a solution? I´m having the same problem
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
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Comment: Log-cpm values from limma
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