Showing : DESEQ2 • reset
1
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6
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1.6k
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Validity of using DESeq2 with directly normalized EDASeq counts rather than offset
deseq2 edaseq
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
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10
replies
1.2k
views
DESEQ2 1.24 versus 1.14
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
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2
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1.4k
views
Coefficient names for multiple group comparisons to use with lfcShrink & apeglm
deseq2 lfcShrink apeglm
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 20
0
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4
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938
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DESeq2 for repeated/clustered samples
deseq2 repeated measures
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
2
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7
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2.4k
views
DeSeq2 - Can't fetch any results: Error in .wrap_in_length_one_list_like_object(value, name, x)
deseq2 software error
updated 12 months ago by • 0 • written 5.9 years ago by ▴ 30
3
votes
3
replies
2.1k
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Issue with scp transfer of DESeq2 objects
deseq2 scp Unix Single-Cell
updated 5.9 years ago by 25k • written 5.9 years ago by ▴ 20
0
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9
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2.2k
views
DESeq2 with nanostring data
deseq2 nanostring
5.9 years ago acs1990 ▴ 10
0
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4
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1.6k
views
ddsClean <- ddsTC[which(mcols(ddsTC)$betaConv),] Error in base::which(x, arr.ind, useNames, ...) : argument to 'which' is not logical
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
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3
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4.2k
views
Normalisation - Deseq2 vs StingTie-Ballgown
deseq2 StringTie RNA-seq normalisation
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
1
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5
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4.5k
views
DESeq2 swap ensembl gene id rownames with gene symbol column
deseq2 dataframe ensembl gene id gene symbol entrezid
updated 8 months ago by • 0 • written 5.9 years ago by ▴ 10
0
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5
replies
1.2k
views
deseq2 differential gene expression and fold change
deseq2
5.9 years ago Jitendra ▴ 10
1
vote
1
reply
669
views
Analyzing mini-bulk samples with DESeq2
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
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1
reply
1.5k
views
Assessing the influence of covariates on RNA-seq in DESeq2
deseq2 rna-sequencing covariates glm
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 20
0
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7
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1.8k
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DESEQ2 for circRNA normalisation
DESEQ2 circRNA normalisation
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
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2
replies
1.2k
views
Differential Expression Analysis on a Subset Derived from a Previous Contrast in edgeR or DESeq2
deseq2 design formula design matrix edgeR ATAC
updated 5.9 years ago by 53k • written 5.9 years ago by • 0
0
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1
reply
1.5k
views
DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2 contrasts reference level
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
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4
replies
1.4k
views
>5000 significantly differentially expressed genes
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
2
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1
reply
3.5k
views
Understanding interactions in DESeq2
deseq2
updated 5.9 years ago by ★ 1.4k • written 5.9 years ago by • 0
0
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2
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1.4k
views
DESeq2 changing Rownames (Gene accession numbers)
deseq2
6.0 years ago JGibbons1 • 0
0
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1
reply
486
views
DESeq2: downregulation of control sample
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
1
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3
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1.5k
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Collapse Technical Replicates and Group-specific condition effects, individuals nested within groups
deseq2 RNAseq model.matrix collapseTechnicalReplicates
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 50
0
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3
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594
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Help with DESeq2 design matrix
deseq2
updated 6.0 years ago by • 0 • written 6.0 years ago by • 0
4
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6
replies
3.4k
views
Does DESeq2 Data_transformation (vsd or rld) Change Clustering (and PCA_plot) Results?
DESeq2 rld vsd data transformation ntd
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
1
reply
580
views
Results counts to Deseq object
deseq2 countmatrix
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
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3
replies
2.4k
views
Comparing factor levels in deseq2
deseq2
6.0 years ago gv ▴ 40
1
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1
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1.0k
views
Normalized counts access in DESeq2 R: with and without batch
deseq2 edger normalization
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 60
2
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6
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1.1k
views
DEseq2 design matrix for paired samples with batch effects
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
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3
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532
views
DESeq2 DE analysis of two samples conditioned on a shared reference
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
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1
reply
1.9k
views
DESeq2 counts function not working
deseq2 Deseq RNAseq
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 10
0
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8
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2.5k
views
DESeq2: experiment with two genotypes and three conditions
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
1
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6
replies
1.4k
views
how to correct for age using Deseq2
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
5
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2
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3.5k
views
How to perform DEseq2 on datasets without replicates or merged replicates
deseq2 R bioconductor RNA_Seq replicates
updated 6.0 years ago by ★ 1.4k • written 6.0 years ago by ▴ 30
0
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3
replies
2.3k
views
DESeq2 using 'relevel' for different comparisons
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 60
2
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3
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965
views
Still lots of NA adjusted p-values in DESeq2 after eliminating Cook's distance cutoff.
deseq2
6.0 years ago ariel ▴ 20
0
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1
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1.5k
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2 RNA-Seq Multifactorial Design GLM Contrasts
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
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7
replies
843
views
DESeq2: Is it possible to have incomplete pairs of samples?
deseq2
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
2
votes
1
reply
955
views
Detecting the power in differential expression
POWER DESEQ2 edger LIMMA DIfferential expression
6.0 years ago Beginner • 0
0
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3
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786
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Nested design vs averaging coefficients
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 40
0
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2
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2.4k
views
WGCNA module Eigengene PC1 and expression correlation
WGCNA DESeq2 RNA-Seq
6.0 years ago Sri Dewi • 0
0
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3
replies
1.2k
views
DESeq2 standalone TE usage
deseq2 normalization
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
3
votes
4
replies
1.2k
views
Error when providing contrast coefficients to lfcShrink() of DESeq2 package
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 90
0
votes
2
replies
751
views
Dynamic allocations possible when building DESeq object?
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 30
1
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10
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11k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 3 months ago by 43k • written 6.0 years ago by • 0
0
votes
2
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3.0k
views
How to overcome negative values obtained from vst for downstream analysis ( calculating bray-curtis and PCoA plot)?
zinbwave deseq2 vegan
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
0
votes
5
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6.1k
views
DEseq Error in checkForExperimentalReplicates
deseq2
6.0 years ago zhezhenwang • 0
0
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4
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3.7k
views
Outliers and Filtering with DESEq2 to overcome NA values in padj
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
2
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3
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1.5k
views
How to correctly set up the design in DESeq2 for RRPP?
deseq2 rrpp DEGs RNAseq
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
6
replies
3.0k
views
CQN to DEseq2
CQN deseq2
updated 3.0 years ago by • 0 • written 6.0 years ago by • 0
0
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1
reply
1.5k
views
Is CQN compatible with DESeq2?
deseq2 cqn
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
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3
replies
1.5k
views
DESeq2 - nested samples (individuals) - time course - conditions
deseq2 nested de
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
4,839 results • Page 44 of 97
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Replies
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much, @ATpoint and @kevin , for your valuable insights. I have carefully checked all your suggestions. First, I examined th…
Answer: Finding duplicated entries in GRangesList by Kevin Blighe ★ 4.0k
The duplicated and unique functions operate element-wise on GRangesList objects. This means that they apply the respective function to each…
Answer: DESeq2 on non-RNASeq counts data by Kevin Blighe ★ 4.0k
The use of DESeq2 for count data from artificial sequences is acceptable, as the program models counts via a negative binomial distribution…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hello Rui Tang, The buffer overflow error in featureCounts that you encountered is likely due to a compatibility issue between the Subre…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
The issue that you describe with the tumor mutational burden (TMB) plots appearing linear and lacking consistent TMB values across samples …
Votes
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
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