Showing : RNAseq • reset
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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
4.0 years ago Yosapol • 0
0
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5
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2.4k
views
RNA-seq with patient samples without replicates with multiple timepoints
edgeR RNASeq multi
updated 4.0 years ago by 53k • written 4.0 years ago by • 0
0
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2
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1.3k
views
How to convert TMM RNA-seq file (generated by edgeR) to list of differentially expressed genes
edgeR DifferentialExpression TMM RNASeq
updated 4.0 years ago by 53k • written 4.0 years ago by • 0
0
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2
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1.4k
views
How similar or disimilar are two sets of DEG?
DESeq2 RNASeq
updated 4.0 years ago by 43k • written 4.0 years ago by ▴ 10
0
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2
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1.9k
views
voom flips the sign relative to log(cpm)
limma limma-voom rnaseq voom
updated 4.1 years ago by 53k • written 4.1 years ago by • 0
0
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1
reply
2.4k
views
Gene expression analysis between three different tissues
DESeq2 RNAseq
updated 4.1 years ago by 68k • written 4.1 years ago by • 0
0
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3
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1.5k
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DEseq2 extracting results from multifactor design
timecourse DESeq2 RNASeq
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
0
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2
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2.3k
views
Should immunoglobulin genes be filtered out during RNA-seq differential expression analysis
RNASeq
updated 19 months ago by • 0 • written 4.1 years ago by • 0
0
votes
1
reply
1.2k
views
Job: Computational Biologist at Chinook Therapeutics
RNASeq Bioconductor Genomics
written 4.1 years ago by • 0
0
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2
replies
2.2k
views
log2FoldChange calculation in DESeq2
DESeq2 RNASeq qPCR qPCRData
4.1 years ago Claire • 0
0
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4
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1.3k
views
Clarify some basic concepts about DESeq normalization
deseq2 rnaseq normalization
written 7.6 years ago by • 0
0
votes
2
replies
2.1k
views
featureCounts: unable to find chromosome in SAM header
RNASeq featureCounts
updated 3.0 years ago by • 0 • written 4.1 years ago by • 0
1
vote
2
replies
1.4k
views
DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq DESeq
4.1 years ago krawczyk.margarita • 0
5
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4
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11k
views
DESeq2: LRT or WALD guidance
DESeq2 RNASeq DifferentialExpression
updated 3.5 years ago by • 0 • written 4.1 years ago by ▴ 10
0
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0
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732
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EventPointer on TCGA RNA-seq
RNASeq EventPointer
4.1 years ago Marie • 0
0
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5
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1.7k
views
DESeq2 shows comparison nonsignificant, unclear why
DESeq2 RNASeq DifferentialExpression
updated 3.1 years ago by 43k • written 4.1 years ago by • 0
4
votes
4
replies
1.6k
views
Raw RNA-seq data: column names are sequences
RNASeq
updated 4.2 years ago by ★ 5.0k • written 4.2 years ago by • 0
0
votes
1
reply
858
views
PCA M3C
M3C RNASeq
updated 4.2 years ago by ★ 4.0k • written 4.2 years ago by • 0
0
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2
replies
1.7k
views
Deseq2 outlier detection (about Cook's distance)
DESeq2 RNASeq DifferentialExpression
4.2 years ago peter.zhouyu • 0
0
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1
reply
1.7k
views
Identify a scRNASeq cell-population using a bulk RNA Seq dataset of that population?
RNASeq rnaseq scRNAseq
updated 4.2 years ago by ★ 29k • written 4.2 years ago by ▴ 10
3
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1
reply
1.2k
views
Compare two samples by Deseqs
DESeq2 RNASeq
updated 4.2 years ago by ★ 4.0k • written 4.2 years ago by ▴ 10
0
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3
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1.4k
views
EdgeR question: why I got discrepancy results for DEGs when using different ways setting up the models
RNAseq edgeR DEGs
updated 3.6 years ago by 53k • written 4.2 years ago by ▴ 380
0
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1
reply
880
views
What is the best approach to analyze RNA-seq data over 3 time points, but with average 60% missing samples in different time points?
RNASeq
updated 4.2 years ago by 68k • written 4.2 years ago by • 0
0
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0
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1.1k
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Job: Computational postdoctoral fellow for cancer disparities research (Boston University)
DNASeq RNASeq SingleCell
4.2 years ago camp ▴ 10
2
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6
replies
4.3k
views
DESeq2 - understanding intercept and contrasts
DESeq2 RNASeq
4.2 years ago sarah-spie ▴ 20
0
votes
3
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1.1k
views
identifying trends in RNA-seq data
RNASeq trend
updated 4.2 years ago by ★ 5.0k • written 4.2 years ago by ▴ 670
0
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4
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1.9k
views
AlignmentsTrack empty plot
Coverage RNASeq plot Gviz
updated 2.7 years ago by 68k • written 4.2 years ago by • 0
0
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0
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887
views
WGCNA out of memory
wgcna RNASeq
4.2 years ago zli1 • 0
0
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14
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3.6k
views
Best practice for quantifying sncRNA
Salmon sncRNA RNASeq
4.2 years ago Abhishek • 0
5
votes
9
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2.3k
views
Time series DE gene analysis with edgeR where specific timepoints have NA levels across different patients
edgeR RNASeq DifferentialExpression TimeCourse
updated 4.2 years ago by 68k • written 4.2 years ago by ▴ 840
2
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6
replies
5.9k
views
How can I use geom_label_repel with EnhancedVolcano?
ggrepel RNASeq R EnhancedVolcano
4.2 years ago Loren ▴ 10
1
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4
replies
7.2k
views
Issues with scaling down enrichplot's dotplot and gseaplot2 plots
RNASeq clusterProfiler enrichplot
updated 3.5 years ago by • 0 • written 4.2 years ago by • 0
3
votes
4
replies
1.8k
views
DRIMSeq: many NAs in results compared to DESeq2 ?
DESeq2 DRIMSeq dtu RNASeq
4.2 years ago sbcn ▴ 80
0
votes
1
reply
1.1k
views
Pseudoalignment for repetitive sequences
Kallisto RNASeq pseudoaligners ShortTandemRepeats
updated 4.2 years ago by 68k • written 4.2 years ago by • 0
1
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3
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1.2k
views
subset a list based on table
edgeR RNASeq resfilt
updated 4.3 years ago by ★ 5.0k • written 4.3 years ago by • 0
2
votes
9
replies
3.3k
views
extract fold change of a list of gene from EdgeR?
EdgeR RNAseq Foldchange
updated 4.3 years ago by ★ 1.4k • written 4.3 years ago by • 0
2
votes
1
reply
965
views
estimateSizeFactors before or after removing non-coding genes and filtering for low counts
DESeq2 RNASeq
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
2
votes
1
reply
9.1k
views
EnhancedVolcano Label Question
RNASeq EnhancedVolcano DEGs
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by • 0
2
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1
reply
1.4k
views
Complex design with paired and unpaired samples with edgeR RNA-seq DE analysis
edgeR RNASeq
updated 4.3 years ago by 53k • written 4.3 years ago by ▴ 780
0
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1
reply
726
views
Creating the correct model to account for paired-samples (patient-effect) help needed!
edgeR limma rnaseq
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
1
vote
1
reply
1.3k
views
DESeq2 for allele-specific expression with contrasts between conditions
DESeq2 AllelicImbalance edgeR RNASeq
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
0
votes
8
replies
2.8k
views
DESeq2: Variable Importance
DESeq2 RNASeq
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
2
votes
4
replies
1.7k
views
RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2 RNASeq BatchEffect limma
updated 2.1 years ago by 43k • written 4.3 years ago by • 0
0
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1
reply
981
views
Query regarding WGCNA module formation
WGCNA RNAseq RNASeqData
updated 4.4 years ago by ▴ 760 • written 4.4 years ago by • 0
0
votes
0
replies
850
views
TCSeq input information
time RNAseq TCSeq
4.4 years ago curiousmind007 ▴ 10
1
vote
5
replies
3.1k
views
Error in stattest function
R rnaseq Ballgown
updated 4.4 years ago by • 0 • written 7.7 years ago by • 0
0
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1
reply
1.7k
views
Filtering DESeq2 results for | LFC | > 1 genes
RNAseq LFC DEseq
4.4 years ago ayy2110 • 0
0
votes
2
replies
2.9k
views
Can't install KEGGprofile
KEGG RNASeq
updated 4.4 years ago by 68k • written 4.4 years ago by • 0
0
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2
replies
2.0k
views
Error in DESeqDataSetFromMatrix()
DESeq2 RNAseq
updated 3.3 years ago by ▴ 10 • written 4.4 years ago by • 0
0
votes
1
reply
1.1k
views
Extracting Go-enrichment and pathway analysis from phytozome annotation file
RNASeq GO
updated 4.4 years ago by 68k • written 4.4 years ago by • 0
1,409 results • Page 7 of 29
Recent ...
Replies
Comment: PCA subset of genes vs DE by Ben • 0
PCA evaluates separation according to your input. The subset of genes you used may be entirely identical in terms of expression, indicatin…
Comment: Problem with MakeTxDbFromGFF by Ben • 0
Wow can't believe he can really answer this [speed stars][1] [1]: https://speed-stars.co
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.
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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