Showing : DEseq2 • reset
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DESEQ2 Batch effect
deseq2 batch
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
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4
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How to analyze RNAseq data with multiple treatment groups and each subject has pre and post-treatment measures using deseq2/edger/limma?
deseq2 limma edger Tutorial
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
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1
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948
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Independent dataset comparison, design definition and average of contrasts in Deseq2
Deseq2 design definition average of contrasts singe-cell
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
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2
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770
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Find the expected counts in DESeq2 output
deseq2
updated 6.7 years ago by ★ 1.4k • written 6.7 years ago by • 0
3
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2
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1.2k
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model matrix design for DESeq2 for use with lfcShrink function
deseq2 model.matrix
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
3
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5
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1.2k
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Accounting for batch effect in DESseq2
deseq2 batch_effect
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 10
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1
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1.2k
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Finding genes that are expressed only in one condition within a contrast
filter deseq2
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 180
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1
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884
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Multiple comparisons with Deseq2
deseq2
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
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1
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4.2k
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DESeq2 coldata and count data subset
deseq2 differential gene expresssion
updated 6.7 years ago by 25k • written 6.7 years ago by • 0
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1
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662
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randomized design (Treatment and time)
deseq2
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
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3
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1.1k
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DEseq2: Why low counts mean count < 804
deseq2
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
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2
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877
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Design definition with multiple conditions in DESeqDataSetFromMatrix
deseq2
6.7 years ago silvia.morini01 • 0
2
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6
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2.6k
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Normalisation for count data visualisation only
deseq2 salmon tximport normalization
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
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1
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1.0k
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DESeq2 : Calculation of rlog (regularized log transformation)
deseq2
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
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8
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4.8k
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DESEQ2 - help with interpreting time series heatmaps and resultsName
deseq2
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
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1
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724
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Contrast argument in DEseq
deseq2
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
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15
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3.6k
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Phyloseq to deseq2
deseq2
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 10
1
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3
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1.4k
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Design matrix: DESeq2
deseq2
6.7 years ago Gyan Prakash Mishra ▴ 10
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1
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737
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Interaction term for condition, time point and genotypes together in DESeq2
deseq2
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
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2
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967
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Usage of interactions for multi-factor analysis
deseq2
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
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2
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1.4k
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DESEQ2: rnaseqGene fisison tutorial time course graph has non-numerical x-axis
deseq2 rnaseqGene
6.7 years ago courtney.stairs • 0
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2
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1.2k
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Indentify DESeq2 is take too long
deseq2
6.7 years ago lucianalpt • 0
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6
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1.8k
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How do I prevent my R kernel (Jupyter Notebook) from dying after running variance stabilizing transformation?
deseq2
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 20
5
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5
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8.3k
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Differential Expression Analysis between conditions of single cell RNA-Seq
deseq2 scRNA-Seq RNA-Seq differential expression analysis
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 60
3
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9
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6.3k
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txi <- tximport(files, type="salmon", tx2gene=tx2gene) Error in tximport(files, type = "salmon", tx2gene = tx2gene) : all(file.exists(files)) is n…
deseq2 tximport file.path files file.exists
6.8 years ago • updated 6.7 years ago Leo K • 0
0
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6
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2.5k
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DESeq2; loading htseq-count output; sample condition is described in a different csv file
deseq2
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
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2
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2.5k
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DeSEQ2- What is the difference between Gene Clustering and using LRT for Time Series experiment WITHOUT treatments
deseq2 Time Series Gene Clustering LRT ATACseq
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
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1
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1.0k
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Significance of the interaction term in DESeq2
deseq2
updated 6.7 years ago by 43k • written 6.7 years ago by ▴ 10
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4
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1.2k
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What will lead DESeq2 shows no DEGs if workflow adopted is okay?
deseq2
updated 6.7 years ago by ▴ 130 • written 6.7 years ago by • 0
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1
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938
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Getting a signature specific to each patient
DESeq2 r cancer
updated 6.7 years ago by 68k • written 6.7 years ago by ▴ 30
1
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5
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2.4k
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Counts Worry: DESeq2: DEGs are from genes with mostly zero across groups
deseq2 DE DEG
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
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7
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2.1k
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Problems with DESeq2 'design' parameter using Shiny/rhandsontable
deseq2 shiny design rhandsontable hot_to_r()
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
1
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2
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677
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DESeq2: Errors in .Call(.NAME, ..., PACKAGE = PACKAGE)
DESeq2 Errors
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
1
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1
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765
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Bringing in data for DESeq2, can't match first column colData to column names of countData
deseq2 bioconductor
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
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5
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3.0k
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Getting opposite log2 fold change
deseq2 gene expression log2foldchange R
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
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2
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1.9k
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Very high threshold for independent filtering
deseq2 mirna independent filtering
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
3
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7
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30k
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DESeq2 log2FC shrink before GSEA or not?
deseq2 gsea rnaseq gene espression
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
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2
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1.1k
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Adjusting DESeq2 p-values through IHW using pathway information as covariate
IHW deseq2 Pathway
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 20
2
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2
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2.3k
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How to extract factor levels of coldata from deseq object?
deseq2 levels factor colData
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 20
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5
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1.1k
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Batch correction with DeSeq2: problem with creating model and getting all conditions
deseq2
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
2
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4
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5.0k
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How to reconfigure Jupyter Notebook to locate specific version of R?
deseq2 software error
6.8 years ago david.wheeler7 ▴ 20
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4
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1.0k
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DESeq2: Second order interactions
deseq2
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
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1
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1.3k
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Using STAR and DESeq2 for circRNA analysis
STAR deseq2
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
4
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10
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7.5k
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Random Effect in DESeq2
deseq2
updated 4.0 years ago by • 0 • written 6.8 years ago by ▴ 20
1
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1
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1.9k
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News: Bioinformatics Summer School - July 2019 - UCLouvain (Belgium)
RNAseq deseq2 proteomics transcriptomics workshop News
written 6.8 years ago by 1.6k
4
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6
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4.6k
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DESeq2 vst normalization: Do I have a heteroscedasticity problem and if so, what can I do about it?
deseq2 normalization rna-seq TCGA vst
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 70
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26
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8.6k
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How can I install DeSeq2 in Jupyter Notebook?
deseq2
updated 6.8 years ago by ▴ 70 • written 6.8 years ago by ▴ 20
0
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1
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733
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Is it required to specify Outliers function in DESeq2
deseq2
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 10
0
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2
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1.5k
views
Different results in DESeq2 when using betaPrior=TRUE and betaPrior=FALSE
deseq2
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 30
0
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9
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2.9k
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NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq deseq2 contrast subgroup
6.8 years ago ariel ▴ 20
4,840 results • Page 53 of 97
Recent ...
Replies
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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