Showing : RNAseq • reset
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Job: Postdoctoral Position: Posttranscriptional gene regulation in T cells (analysis of RNAseq, metabolomics)
Basel switzerland RNAseq metabolomics Job
7.5 years ago Robert Ivanek ▴ 750
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4
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5.9k
views
Change point size and remove outline in scater's plotPCA
scater rnaseq single-cell
updated 7.5 years ago by • 0 • written 8.4 years ago by ▴ 70
3
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2
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2.0k
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Repeated Measures, Within-Subject, Between-Groups RNAseq Analysis
edgeR rnaseq repeated measures
updated 7.5 years ago by ★ 7.9k • written 7.5 years ago by • 0
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1
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2.0k
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Error while Installing DESeq2
software error R deseq2 rnaseq
updated 7.5 years ago by 43k • written 7.5 years ago by • 0
2
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18
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4.2k
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Using tximport on rsem files produces error while trying to read in files
R tximport rnaseq tpm rsem
7.5 years ago stephan.emmrich ▴ 10
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1
reply
670
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Time-series Experiments with Varied Drug Concentrations Design Matri
deseq2 rnaseq
updated 7.5 years ago by 43k • written 7.5 years ago by • 0
1
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1
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1.4k
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DESeq2 confounding cartridge
deseq2 confounders nanostring rnaseq differential gene expression
updated 7.5 years ago by 43k • written 7.6 years ago by • 0
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2
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3.9k
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Going crazy with normalizing TCGA raw rsem gene count
cancer tcga normalization rnaseq differential gene expression
updated 7.6 years ago by • 0 • written 10.5 years ago by • 0
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1
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1.3k
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How to compare RNA-seq counts matrices from different aligners ?
rnaseq counts alignement
7.6 years ago Aurora ▴ 20
7
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8
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15k
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DESeq2: one condition vs multiple combined
rnaseq deseq2
updated 7.6 years ago by ▴ 10 • written 9.2 years ago by ▴ 40
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0
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2.7k
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
7.6 years ago digrigor ▴ 10
0
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28
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4.5k
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Job: Postdoc on integrating and analyzing new transcriptome types in the Bgee database
rnaseq data integration single-cell pacbio across species Job
7.6 years ago bgee • 0
0
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1
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1.3k
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GenomicFeatures: could not find symbol "recursive" in environment of the generic function
genomicfeatures rnaseq txdb
7.6 years ago lucasmacielbiotec • 0
1
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4
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3.2k
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If transcript-to-gene conversion is needed in kallisto > tximport > DESeq2 pipeline
deseq2 rnaseq kallisto tximport
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
7
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10
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7.6k
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Justification for collapsing technical replicates in DESeq2
deseq2 rnaseq replicate differential expression
updated 7.6 years ago by ▴ 30 • written 9.2 years ago by ▴ 50
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5
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1.3k
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DESeq2: normalization of experiments sequenced separately
RNAseq normalization deseq2
7.6 years ago uguy • 0
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0
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1.4k
views
Job: Biostatistician III @ Duke University
rnaseq precision medicine biomarker genomics Job
7.6 years ago ram330 • 0
1
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1
reply
843
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edgeR: Subset DGEList by treatment-specific expression
rnaseq edger
updated 7.6 years ago by ★ 29k • written 7.6 years ago by • 0
7
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11
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3.3k
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Analysis of pathways using edgeR
rnaseq differential expression edgeR kegg
updated 7.6 years ago by 53k • written 7.6 years ago by ▴ 60
2
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2
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1.8k
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ASpli ERROR during the counting step
ASpli rnaseq
updated 7.6 years ago by ▴ 10 • written 7.9 years ago by ▴ 10
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2
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3.3k
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use tximport's countsFromAbundance when using DESeq2
deseq2 tximport normalization salmon rnaseq
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
1
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3
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1.4k
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plotMA (DESeq2) Issue
deseq2 plotMA rnaseq logfoldchange
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
0
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0
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607
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summarizeOverlaps to count stranded single-end RNA-seq dara
rnaseq
7.6 years ago yinyuan • 0
1
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4
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2.0k
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problem of getting count matrix in featurecounts of Rsubread package
rnaseq rsubread featurecounts
updated 7.6 years ago by ★ 3.6k • written 7.6 years ago by • 0
2
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2
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1.5k
views
tximport failing at importing TPM instead of FPKM
tximport rnaseq rsem
updated 7.6 years ago by • 0 • written 7.6 years ago by • 0
5
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4
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2.1k
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Glimma Interactive plots for RNAseq
Glimma R markdown rnaseq
7.6 years ago Aurora ▴ 20
2
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2
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963
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Normalize for changes in one direction
limma voom rnaseq
updated 7.6 years ago by ★ 29k • written 7.6 years ago by ▴ 90
2
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1
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1.1k
views
DESeq2-No replicates-Utility of log2fold shrunk values?
deseq2 rnaseq
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
0
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8
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6.5k
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Comparing between two differential expression analysis - two different fold changes
Deseq deseq2 differential gene expression rnaseq statistical test
7.7 years ago Marina ▴ 40
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2
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4.3k
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DESeq2 followed by goseq GO-analysis: Extracting DE genes of enriched GO category
deseq2 goseq rnaseq go enrichment differential gene expression
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
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4
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1.8k
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Normalise counts when tumour samples have normal tissue contamination.
deseq2 deseq edgeR rnaseq htseqcounts
7.7 years ago Deepali • 0
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0
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1.6k
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Job: Senior Bioinformatician, Children's Cancer Research Institute Vienna, Austria
postdoc rnaseq NGS WGS bioinformatician job Job
7.7 years ago da.de ▴ 30
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1
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1.9k
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MA plot interpretation .
MAPLOT DESEQ2 RNASEQ
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
5
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9
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4.2k
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Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb ensembl release rnaseq salmon tximport
7.7 years ago emmak ▴ 20
3
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4
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2.7k
views
edgeR - comparing treatment groups across multiple populations
rnaseq edger
updated 7.7 years ago by ★ 29k • written 7.7 years ago by • 0
1
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3
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998
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rna-seq analysis with limma shows only 1 differential expressed gene
limma rnaseq
updated 7.7 years ago by • 0 • written 7.7 years ago by • 0
4
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7
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3.6k
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DESeq2 vs TCGAbiolinks normalization methods
normalization rnaseq deseq2
updated 3.9 years ago by • 0 • written 7.7 years ago by ▴ 420
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1
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2.4k
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How can I retrieve the gene names of my count matrix?
rnaseq summarizeoverlaps count matrix
updated 7.7 years ago by 68k • written 7.7 years ago by • 0
3
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4
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3.4k
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DESeq2 batch effect modeling and matrix not full rank
deseq2 rnaseq rna-seq
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 20
2
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2
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1.1k
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Moderated F-statistics for time course experiment
limma rnaseq
updated 7.7 years ago by 53k • written 7.7 years ago by ▴ 130
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0
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1.1k
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Subset functionin R
R ballgown rnaseq
7.7 years ago amy16 • 0
0
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4
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1.2k
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can DESeq2 be used to compare these miRNA read counts from 9 samples?
deseq2 rnaseq
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
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0
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1.1k
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Accessing the assembly data-output
R rnaseq ballgown
7.7 years ago amy16 • 0
1
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1
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1.4k
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Expression deconvolution using PSEA: applicable to RNA-seq?
deconvolution rnaseq psea
7.7 years ago WouterDeCoster ▴ 130
1
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1
reply
2.6k
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WGCNA - Choosing the best threshold
wgcna sft picksoftthreshold threshold rnaseq
updated 7.7 years ago by ★ 3.0k • written 7.7 years ago by ▴ 40
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5
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3.1k
views
MasigPro and estimation of theta for negative binomial law
R masigpro edgr rnaseq negative binomial model
7.7 years ago nicolas.hipp ▴ 20
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3
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1.5k
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upperquartile with voom
limma-voom rnaseq normalization
7.7 years ago bilcodygm • 0
0
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2
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1.6k
views
assess quality of data
rnaseq edger limma-voom
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
2
votes
2
replies
2.3k
views
RNAseq analysis: how to compare two very different samples?
edgeR deseq2 RNAseq
updated 7.7 years ago by ★ 29k • written 7.7 years ago by ▴ 10
1
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3
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847
views
Is it reasonable to use rlog difference to reflect differential expression of a gene across samples, and rlog value to reflect the expression level
deseq2 rnaseq
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
1,409 results • Page 14 of 29
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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