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Answer: Answer: Slightly different count plots from R and spreadsheet
6 hours ago Michael Love 42k
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80
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Answer: Answer: How to run allelic imbalance in apeglm
2 days ago Michael Love 42k
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1
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584
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Answer: Answer: Numerical differences in DESeq2 output depending on different design matrix cons
4 days ago Michael Love 42k
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202
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Answer: Answer: DESeq2- Mysterious interaction suppresses DEGs
4 days ago Michael Love 42k
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303
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Answer: Answer: Can DESeq2 rlog normalized matrix reflects time course result directly?
7 days ago Michael Love 42k
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147
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Answer: Answer: Assymetric MA plot with no overall trend
8 days ago Michael Love 42k
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115
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Answer: Answer: normalization across different species for DESeq2 analysis
8 days ago Michael Love 42k
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544
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Answer: Answer: Can I trust the differential expression analysis when the two groups overlap on
8 days ago Michael Love 42k
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158
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Answer: Answer: How to save the DEXSeq results
16 days ago Michael Love 42k
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152
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Answer: Answer: Trim/Filter out-of-bounds GRanges
16 days ago Michael Love 42k
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197
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Answer: Answer: Handling multiple differential expression comparisons
17 days ago Michael Love 42k
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176
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Answer: Answer: DESeq2 v1.35.0
20 days ago Michael Love 42k
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309
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Answer: Answer: log2FoldChange value is way too different when compared with counts(dds)
21 days ago Michael Love 42k
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161
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Answer: Answer: Fold change calculation in Diffbind vs. DESEQ2?
22 days ago Michael Love 42k
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174
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Answer: Answer: Timecourse RNASeq analysis
22 days ago Michael Love 42k
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142
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Answer: Answer: Padj "NA" with thousands of low count although the raw read counts are quite lar
22 days ago Michael Love 42k
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230
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Answer: Answer: PCA plot suggestions
26 days ago Michael Love 42k
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260
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Answer: Answer: Deseq2. decontXcounts not integers. Useful alternative?
26 days ago Michael Love 42k
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168
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Answer: Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
27 days ago Michael Love 42k
2
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331
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Answer: Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
28 days ago Michael Love 42k
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257
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Answer: Answer: DESeq2 - dispersion estimation when there is none
4 weeks ago Michael Love 42k
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160
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Answer: Answer: rlog transformation
4 weeks ago Michael Love 42k
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133
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Answer: Answer: ONT long-read RNA sequencing - data analysis options
4 weeks ago Michael Love 42k
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1
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763
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Answer: Answer: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
4 weeks ago Michael Love 42k
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151
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Answer: Answer: covariate with negative and positive values
4 weeks ago Michael Love 42k
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269
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Answer: Answer: How to retrieve detailed regression results from deseq2
5 weeks ago Michael Love 42k
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296
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Answer: Answer: DEG with low counts
5 weeks ago Michael Love 42k
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250
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Answer: Answer: Interaction term vs grouping variable design considerations
6 weeks ago Michael Love 42k
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196
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Answer: Answer: IgG control in RIP-seq with Deseq2
6 weeks ago Michael Love 42k
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267
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Answer: Answer: Regressing out batch effects
6 weeks ago Michael Love 42k
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174
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Answer: Answer: DESeq2 , filter and theta arguments in resutlts()
7 weeks ago Michael Love 42k
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293
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Answer: Answer: Abnormal Low Dispersion Gene Population in DESeq2
7 weeks ago Michael Love 42k
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196
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Answer: Answer: Convert transcriptomic bam to genomic bam?
7 weeks ago Michael Love 42k
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176
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Answer: Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
7 weeks ago Michael Love 42k
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1
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378
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Answer: Answer: Doing comparison of RNA-seq data using Deseq2
7 weeks ago Michael Love 42k
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0
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377
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Answer: Answer: PCA of different bacterial species
8 weeks ago Michael Love 42k
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1
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220
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Answer: Answer: Clarification on Library Size Normalization After Using tximport with countsFrom
8 weeks ago Michael Love 42k
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188
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Answer: Answer: collapseReplicates dimension error
8 weeks ago Michael Love 42k
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1
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253
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Answer: Answer: DESeq2 "Contrast" option
8 weeks ago Michael Love 42k
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283
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Answer: Answer: Filtering and Reference Level for DESeq2
8 weeks ago Michael Love 42k
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321
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Answer: Answer: DESeq2 - Plot Nr. Genes vs Variance explained in PCA
9 weeks ago Michael Love 42k
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295
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Answer: Answer: Help with Complex DESeq2 Design
9 weeks ago Michael Love 42k
1
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199
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Answer: Answer: Need help with creating and plotting temporal clustering analysis of DEGs
9 weeks ago Michael Love 42k
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158
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Answer: Answer: Help with DESeqDataSetFromHTSeqCount
9 weeks ago Michael Love 42k
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224
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Answer: Answer: lfcShrink error: the line search routine failed
9 weeks ago Michael Love 42k
0
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307
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Answer: Answer: RNAseq analysis
9 weeks ago Michael Love 42k
2
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248
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Answer: Answer: With DESeq2 "Not full rank" Error with design
9 weeks ago Michael Love 42k
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350
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Answer: Answer: Missing Band on Volcano Plot from DESeq2
9 weeks ago Michael Love 42k
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1
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436
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Answer: Answer: DESeq2: subtract effect of an isotope control before comparing to a baseline sam
9 weeks ago Michael Love 42k
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0
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468
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Answer: Answer: DESeq2 filtering vs edgeR filtering
10 weeks ago Michael Love 42k
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