Showing : DESEQ2 • reset
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DESeq2 ratio of ratios and p-value
DESeq2 dese
4.1 years ago • updated 4.0 years ago wilfried.guiblet • 0
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8
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1.9k
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DESeq2 cannot relevel
DESeq2
4.1 years ago • updated 4.0 years ago Jorge • 0
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5
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2.0k
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DESeq2: error while ploting figure
R DESeq2
updated 4.0 years ago by 43k • written 4.1 years ago by • 0
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3
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2.4k
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DeSeq2 Comparing One group vs Two groups
DESeq2
written 4.1 years ago by ▴ 10
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6
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2.3k
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Batch effect from to sequencing data at differents depths
Sequencing sequencingDeepth BatchEffect DESeq2
4.1 years ago ary.lech ▴ 10
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1
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2.3k
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DESeq2 rows did not converge in beta, how to solve
DESeq DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
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4
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2.0k
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DESeq2/edgeR/limma help with most appropriate design matrix
DESeq2 limma modelmatrix edgeR designmatrix
updated 4.1 years ago by 53k • written 4.1 years ago by • 0
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1.0k
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lfcshrink() and 2 conditions, 3 genotypes
lfcshrink DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
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1
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654
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Interaction model genes don't intersect
DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
3
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3
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1.0k
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Is comparison of data without pairwise comparison in batches possible? Or even reasonable?
RNASeq DESeq2
updated 4.1 years ago by 68k • written 4.1 years ago by ▴ 20
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1.5k
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DESeq2 normalization when using with derfinder
Normalization DESeq2 derfinder
4.1 years ago Debayan ▴ 20
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2
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1.7k
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Correct workflow for analyzing differentially expressed genes and correlation analyses on TCGA data?
DESeq2
4.1 years ago mario.keller.1988 ▴ 20
4
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1
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3.1k
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mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene RNASeqR DESeq2 RNAseq
updated 4.1 years ago by 43k • written 4.1 years ago by ▴ 10
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4
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1.3k
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Error in designing DESeq2 time pointed experiments
LTR DESeq2
4.1 years ago AZ ▴ 30
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2
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1.2k
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results() function and finding the difference of differences
interactions DESeq2
4.1 years ago Nayrouz • 0
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970
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DESEQ2 when global gene expression changes exist
DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
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2
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1.7k
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DESeq2 PlotCounts() function
DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
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3
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1.6k
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DESeq2 Design Matrix Two Conditions and Two Treatments
designmatrix deseq2 DESeq2
updated 4.1 years ago by ★ 1.4k • written 4.1 years ago by • 0
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2
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7.7k
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Interpretation of Log 2 fold change
DESeq2
4.1 years ago adeler001 • 0
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2
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2.1k
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Installing DESEq2 Error: unable to access index for repository https://bioconductor.org
Install Bioconductor DESeq2
4.1 years ago ladypurrsia ▴ 10
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2
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3.2k
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DESeq2 version
DESeq2
4.1 years ago adeler001 • 0
2
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3
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2.0k
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Contrast treated samples against both scramble and untreated controls
design contrast DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
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4
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1.2k
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How to analyze 10 samples (5 control, 5 treatment) which perform the experiment from different day
DESeq2 RNASeq
4.1 years ago Yosapol • 0
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6
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2.2k
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DESeq2 Normalization
DESeq2
4.1 years ago Jamie • 0
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2
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1.3k
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DESeq function stuck on estimating gene-wise dispersion.
DESeq2
4.1 years ago m.deluca • 0
1
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1
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827
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Multiple samples per individual
DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by ▴ 50
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4
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2.5k
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Model matrix not full rank, then
DESeq2
4.1 years ago Sonia • 0
2
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1
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2.6k
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How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?
DESeq2 tximport Kallisto TMM edgeR
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
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3
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1.7k
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small log2foldChange value in the most significant genes
DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
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1
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1.0k
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Need of some clarifications
TimeCourse DifferentialExpression DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by ▴ 30
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2
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1.3k
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Deseq2 Resul variation by LFC variation
rnaseqGene DESeq2 Transcriptomics
4.1 years ago • updated 2.5 years ago diangomaiga • 0
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2
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946
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where the gene is overexpressed and down regulated while doing DESeq2 analysis
DESe DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
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3
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Is it advisable to input a count matrix that consists of reads aligned using different algorithms (HT-Seq and Salmon)?
DESeq2
updated 4.1 years ago by ★ 1.4k • written 4.1 years ago by • 0
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Using DESeq2 for Differential Expression Analysis with Interaction Term
DifferentialExpression GeneExpression DESeq2 Design()
4.1 years ago p.l.chen • 0
2
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5
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6.9k
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using DESeq2 for ATAC analyses
ATACSeq DESeq2
updated 3.3 years ago by ▴ 20 • written 4.1 years ago by ▴ 20
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2
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1.1k
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Extracting the LFC from a reduced model
DESeq2
4.1 years ago Sonia • 0
2
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2
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9.1k
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Deseq2 and log2foldchange cutoffs- How to get differentially expressed genes?
DifferentialExpression GeneExpression DESeq2 R
updated 4.1 years ago by ★ 5.0k • written 4.1 years ago by ▴ 10
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2
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2.5k
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DESeq2 differential expression analysis of protein coding genes only
DESeq2
updated 4.1 years ago by ★ 5.0k • written 4.1 years ago by • 0
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3
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1.4k
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DESeq2 design formula
DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
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3
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4.5k
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DESeq2 error in design~ code
DESeq2
4.1 years ago Abdou-samad • 0
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8
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2.2k
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Three conditions and two time points
DifferentialExpression DESeq2 time
4.1 years ago AZ ▴ 30
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4
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4.8k
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Question on the fold change estimate
DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
2
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4
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1.5k
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Remove genes in a list from cts
DESeq2
updated 4.1 years ago by ★ 1.4k • written 4.1 years ago by ▴ 50
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5
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DESeq2: All samples have 0 counts for all genes. check the counting script
DESeq2 RStudio
4.1 years ago Sonia • 0
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4
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6.0k
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Conversion from FPKM,RPKM to tpm
DESEQ2 fpkm rpkm tpm
4.1 years ago Sandhiya • 0
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6
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2.6k
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Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r DESeq DESeq2
4.1 years ago s-rhussien • 0
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4
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1.6k
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Can DESeq2 be applied on gene coverages, rather than read counts?
Coverage DESeq2
4.1 years ago Rui ▴ 10
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2.7k
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Nested, multifactorial design formular for targeted contrast of a factor interaction
DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
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3
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1.1k
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[DESeq2] interaction term
DESeq2
updated 4.1 years ago by 43k • written 4.2 years ago by • 0
1
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1
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1.1k
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DESeq2 LRT test without a fixed base reference
DESeq2
updated 4.1 years ago by 43k • written 4.2 years ago by • 0
4,838 results • Page 26 of 97
Recent ...
Replies
Answer: mzR-Rcpp compiler version issue by Laurent Gatto 1.6k
There are two issues here. First, a warning about mzR, that you can safely ignore. It tells you that mzR was compiled using a different …
Comment: Identifying differentially expressed genes in individual samples from a large co by jamie.gearing ▴ 60
Great. Yes, something descriptive is probably good enough, even if the p-values themselves are not so rigorous. Thanks very much Gordon!
Comment: Co-occurrence Network Analysis between Algae and Bacteria by Stefano Mangiola ▴ 40
Just a placeholder, that we are extending `sccomp` to co-occurrence analyses. Yours could be a good use-case to test first. We will be in t…
Answer: DESeq2 design for haplotype MPRA by aimesd808 • 0
I appreciate you telling me about this. Now it's crystal plain to me. Publish this: https://support.bioconductor.org/p/9162649/ [fnf][1] …
Answer: Extract snp information from genomic regions with biomaRt -> "oaries_snp" by Kevin Blighe ★ 4.0k
My sincere apologies that my colleagues had ignored your question. The error occurs because the "chromosomal_region" filter is not valid…
Votes
Answer: Identifying differentially expressed genes in individual samples from a large co
Answer: Identifying differentially expressed genes in individual samples from a large co
Bioconductor Seminar Series - Dec 2: Deep-learning Gene Perturbation Effect Prediction
Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Comment: Error installing Seqinfo
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