Showing : RNA-Seq • reset
12
votes
10
replies
9.2k
views
Pre-processing RNA-seq data (normalization and transformation) for GSVA
gsva gene set variation analysis normalization transformation rna-seq
7.5 years ago • updated 6.7 years ago rached ▴ 60
0
votes
3
replies
2.0k
views
How to handle replicates and treatment conditions in TissueEnrich package
rna-seq TissueEnrich tissue-specific expression differential expression
updated 6.7 years ago by ▴ 10 • written 6.7 years ago by • 0
0
votes
0
replies
1.3k
views
Job: Postdoc in Bioinformatics (UCSF Benioff Children's Hospital Oakland)
Bioinformatics RNA-seq Postdoc Genomics Statistical model Job
6.7 years ago djawaheer • 0
4
votes
4
replies
3.1k
views
Average read counts and batch-effect correction in edgeR
edgeR batch-effect RNA-seq read counts ngs
updated 6.7 years ago by ★ 29k • written 6.7 years ago by ▴ 20
0
votes
3
replies
1.5k
views
Reverse Normalized RNA-seq readcounts/fpkm values to raw readcounts
RNA-seq deseq2 normalization readcount reverse
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
0
votes
5
replies
2.3k
views
DESeq2 package : Error in checkFullRank(modelMatrix) while designing multi factor
DESeq2 multiple factor design design model design matrix rna-seq
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
5
votes
2
replies
2.1k
views
Correct usage of tximport counts in edgeR without offset matrix.
tximport edgeR rna-seq
updated 6.8 years ago by 68k • written 6.8 years ago by • 0
2
votes
3
replies
2.6k
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon edaseq rna-seq deseq2
updated 6.9 years ago by 43k • written 6.9 years ago by ▴ 30
0
votes
0
replies
835
views
Job: RNA Computational Biologist at Panorama Medicine in Philadelphia
rna-seq Job
6.9 years ago Jeremy Leipzig ▴ 70
0
votes
6
replies
2.1k
views
Which sequencing parameters are required for SGSeq analysis of splice events?
rna-seq alternative splicing SGSeq
6.9 years ago andrea.bast • 0
4
votes
4
replies
2.7k
views
Unexpected MAplot after apeglm shrinkage in DESeq2
apeglm deseq2 rna-seq
updated 6.9 years ago by 43k • written 6.9 years ago by ★ 4.9k
7
votes
7
replies
2.2k
views
Using GenomicDataCommons R package to identify cases with both DNA methylation and gene expression data
R gdc rna-seq dna methylation
updated 7.0 years ago by 21k • written 7.0 years ago by ▴ 50
1
vote
6
replies
1.6k
views
Actually meaning of log2FoldChange, p-value & padj in DESeq2 results
deseq2 rna-seq
7.0 years ago hffqyd • 0
0
votes
3
replies
1.6k
views
Strange lfcShrink plot when running DESeq2 workflow
DESeq2 rnaseq rna-seq deseq2 deseq
7.0 years ago Ben ▴ 50
5
votes
7
replies
4.5k
views
Deseq2 design for one condition over 8 different time point
deseq2 rna-seq design matrix deseq
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 10
3
votes
12
replies
7.2k
views
Batch correction when only some subjects have replicates across batches
limma batch effect rna-seq
updated 7.0 years ago by ★ 3.0k • written 7.0 years ago by ▴ 10
0
votes
5
replies
1.8k
views
RNA-seq time course experiment - DESEq2 Contrasts
deseq2 rna-seq interactions contrast
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 10
6
votes
5
replies
2.9k
views
Incorporating subject ID as random effect for repeated measures RNA-Seq analysis
limma rna-seq mixed model repeated measures
updated 7.0 years ago by 53k • written 7.0 years ago by ▴ 280
0
votes
2
replies
1.9k
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2 combat sva rna-seq
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
2
votes
8
replies
3.4k
views
time series, block by patient, between and within comparisons limma-voom
rna-seq time series patient limma-voom
updated 7.1 years ago by ★ 29k • written 7.1 years ago by ▴ 90
2
votes
0
replies
600
views
sharing BiocWorkshops 2018
RNA-seq
7.1 years ago Bogdan ▴ 670
15
votes
12
replies
3.3k
views
ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like they should be markers
deseq2 ZINB-WaVE single cell RNA-seq differential expression
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 60
0
votes
8
replies
2.7k
views
DESeq2 Multi factor, multi time point comparison design formula
rna-seq deseq2 deseq R
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
3
votes
1
reply
1.2k
views
DESeq2: Handling batch effects with only one control replicate coming from another batch
deseq2 rna-seq
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
0
votes
0
replies
1.4k
views
Job: 2 Postdoc Positions in computational epigenetics and non-coding RNA analysis (#CNPD08)
bioinformatician job rna-seq chipseq gsea python Job
7.2 years ago l.brown ▴ 10
0
votes
3
replies
1.4k
views
time series RNA-seq allowing time offset between individuals
edgeR deseq2 rna-seq timecourse fittimeseries
updated 7.2 years ago by ★ 29k • written 7.2 years ago by • 0
1
vote
2
replies
1.0k
views
some questions about using the rlog function of DEseq2
deseq2 rna-seq
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
0
votes
0
replies
1.3k
views
problem for constructing Topological Overlap Matrix (TOM) in WGCNA Algorithm
wgcna RNA-seq Topological Overlap Matrix
7.3 years ago • updated 7.2 years ago modarzi ▴ 10
2
votes
7
replies
2.2k
views
Transcript abundance estimation for time-course RNA-seq data
rna-seq salmon alpine transcript expression
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 20
0
votes
3
replies
1.2k
views
3x2 comparisons in DEseq - time (3 time points) and two treatments
deseq2 deseq rna-seq multiple comparisons
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 60
5
votes
1
reply
1.4k
views
DE analysis when large portion of transcriptome is changed
rna-seq edger ebseq differential expression
updated 7.3 years ago by ★ 29k • written 7.3 years ago by • 0
1
vote
2
replies
1.8k
views
Problem for downloading data from Genomic Data Commons portal via TCGAbiolinks package
TCGAbiolinks RNA-seq
7.3 years ago modarzi ▴ 10
0
votes
0
replies
1.3k
views
Problem for Splitting reverse and forward reading in my RNA-seq
RNA-seq SRA reverse reads forward reads
7.3 years ago modarzi ▴ 10
5
votes
7
replies
3.4k
views
problem for Using RNA-seq data-set in WGCNA
WGCNA RNA-seq
updated 7.3 years ago by ★ 3.0k • written 7.3 years ago by ▴ 10
0
votes
0
replies
1.0k
views
How to manage self loop in gene coexpression network constructed using Pearson correlation in Cor() function
rna-seq gcn desq2 pearsoncorrelation
7.3 years ago aishu.jp ▴ 30
0
votes
3
replies
4.3k
views
Handling pseudogenes in RNA-seq
rna-seq pseudogenes STAR counts
updated 7.3 years ago by ★ 1.1k • written 7.3 years ago by • 0
1
vote
2
replies
1.5k
views
Filtering Rna-seq counts
rna-seq filtering
updated 7.4 years ago by 53k • written 7.4 years ago by ▴ 20
1
vote
4
replies
2.3k
views
DESeq2 design formula - how to account for donor and /or sample?
deseq2 multiple factor design rna-seq
updated 7.4 years ago by ★ 1.4k • written 7.4 years ago by • 0
1
vote
1
reply
1.5k
views
Controlling for batch after Salmon-Tximport
deseq2 wgcna salmon rna-seq DESeq2
updated 7.4 years ago by 68k • written 7.4 years ago by • 0
6
votes
6
replies
7.9k
views
strange results with featureCounts
RNA-seq featureCounts total RNA
updated 3.0 years ago by ▴ 200 • written 7.4 years ago by ▴ 10
0
votes
3
replies
1.4k
views
Analyzing a subgroups of samples, which result should I trust
deseq2 rna-seq
written 7.4 years ago by ▴ 20
1
vote
5
replies
1.6k
views
Comparing RNA-Seq expression data from different sequencers (HiSeq3000 and NovaSeq6000) - are there methods for batch effect corrections?
deseq2 rna-seq illumina batch effect
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 40
3
votes
5
replies
2.2k
views
EdgeR: Prior degrees of freedom effect on tag wise dispersion
R edgeR rnaseq rna-seq
updated 7.5 years ago by ★ 29k • written 7.5 years ago by ▴ 20
2
votes
1
reply
3.5k
views
MAST: testing differential expression with a nested factorial design
MAST single-cell rna-seq
updated 7.5 years ago by ▴ 280 • written 7.5 years ago by ▴ 20
3
votes
7
replies
3.3k
views
novice: building gene co-expression network using RNA-Seq data
rna-seq WGCNA deseq method coexpression
updated 7.5 years ago by ★ 3.0k • written 7.5 years ago by ▴ 10
0
votes
3
replies
2.3k
views
error: NA counts not permitted
systempiper edger rna-seq
updated 7.5 years ago by ★ 29k • written 7.5 years ago by • 0
0
votes
1
reply
3.9k
views
how to infer missing PAM50 molecular subtypes in TCGA-BRCA dataset downloaded with TCGABiolinks?
tcgabiolinks tcga-brca gdc pam50 rna-seq
7.5 years ago pfrancislyon • 0
3
votes
7
replies
6.5k
views
What does this error mean? - issue implementing SVA
sva rna-seq
updated 7.5 years ago by ▴ 30 • written 9.7 years ago by ▴ 40
2
votes
3
replies
2.1k
views
RNA-seq: Time-course data normalisation with TPM
rna-seq normalization deseq2 TPM
updated 7.6 years ago by 43k • written 7.6 years ago by ▴ 10
0
votes
0
replies
700
views
Pipeline to find Kozak sequence in RNAseq data and in silico translation
rna-seq
7.6 years ago csijst • 0
418 results • Page 5 of 9
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Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 4.9k
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 ★ 4.9k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Comment: R course in Boston December 19-20 by eja.gaasa2e.r.m • 0
The upcoming XLSolutions R course in Boston on December 19 20 is a great opportunity to enhance your data skills. Whether you re a beginner…
Answer: Gatins Set error by James W. MacDonald 68k
`GatingSet` isn't a function in `flowCore`. It is however in `flowWorkspace`, which you would need to load first.
Answer: How to model DE for RNA-seq in concordant monozygotic twins? by Gordon Smyth 53k
Your question is more about science than it is about software syntax, and I can't give advice about how to conduct a scientific analysis, n…
Votes
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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