Showing : RNA-SEQ • reset
2
votes
3
replies
192
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 3 days ago by 48k • written 7 days ago by • 0
0
votes
3
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227
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 21 days ago by ★ 1.9k • written 21 days ago by • 0
0
votes
2
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1.4k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 22 days ago by • 0 • written 17 months ago by • 0
3
votes
4
replies
342
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
6 weeks ago Eva ▴ 10
0
votes
10
replies
1.7k
views
Error in reading data on isoformswitchanalyzeR
isoformswitchanalyzeR rna-seq splice-variants
written 4.5 years ago by • 0
0
votes
3
replies
365
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 3 months ago by 40k • written 3 months ago by • 0
5
votes
7
replies
563
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 3 months ago by 48k • written 3 months ago by ▴ 10
0
votes
2
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883
views
Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 4 months ago by • 0 • written 2.9 years ago by • 0
0
votes
3
replies
414
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 4 months ago by 63k • written 4 months ago by • 0
0
votes
3
replies
381
views
Is the gene-specific PCR efficiency a serious concern for intrasample comparisons in RNA-Seq?
RNA-Seq normalization PCR_efficiency bias intrasample_comparison
updated 4 months ago by 63k • written 4 months ago by • 0
1
vote
1
reply
483
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 5 months ago by ★ 3.4k • written 5 months ago by • 0
0
votes
1
reply
272
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 5 months ago by 63k • written 5 months ago by • 0
2
votes
2
replies
376
views
Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 5 months ago by ★ 3.4k • written 6 months ago by • 0
0
votes
1
reply
305
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
7 months ago Jenny Drnevich ★ 2.0k
1
vote
4
replies
659
views
Nested paired design with covariates in limma
RNA-seq Nested paired design limma
updated 7 months ago by 48k • written 3.5 years ago by • 0
4
votes
8
replies
1.5k
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
updated 7 months ago by 63k • written 3.3 years ago by ▴ 30
0
votes
1
reply
420
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 9 months ago by 40k • written 10 months ago by • 0
4
votes
6
replies
5.1k
views
strange results with featureCounts
RNA-seq featureCounts total RNA
updated 11 months ago by ▴ 20 • written 5.4 years ago by ▴ 10
5
votes
9
replies
1.2k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
14 months ago Yang Shi ▴ 10
2
votes
2
replies
745
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
14 months ago Yang Shi ▴ 10
0
votes
0
replies
584
views
Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
14 months ago eolson • 0
2
votes
2
replies
616
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 14 months ago by 48k • written 14 months ago by • 0
3
votes
2
replies
3.8k
views
Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
updated 16 months ago by ▴ 10 • written 3.1 years ago by ▴ 80
5
votes
5
replies
1.2k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
19 months ago • updated 16 months ago 9906201a ▴ 20
3
votes
3
replies
2.6k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 18 months ago by ▴ 30 • written 4.7 years ago by ▴ 30
0
votes
2
replies
3.3k
views
Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage gage package pathview rna-seq
updated 18 months ago by • 0 • written 5.6 years ago by • 0
1
vote
5
replies
1.3k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
19 months ago Lucy ▴ 60
1
vote
3
replies
953
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 19 months ago by 40k • written 19 months ago by • 0
5
votes
2
replies
17k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
updated 20 months ago by • 0 • written 4.7 years ago by ▴ 30
0
votes
5
replies
2.5k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 20 months ago by ★ 3.4k • written 2.5 years ago by • 0
0
votes
1
reply
682
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 20 months ago by 48k • written 20 months ago by • 0
0
votes
7
replies
2.2k
views
Error reading kallisto files using tximport for cross species RNA-Seq analysis
kallisto tximport RNA-Seq across species
updated 22 months ago by • 0 • written 6.3 years ago by ▴ 40
5
votes
12
replies
4.7k
views
DESeq2 time series contrasts between timepoints
rna-seq deseq2
updated 23 months ago by ▴ 30 • written 6.0 years ago by ▴ 40
1
vote
1
reply
2.0k
views
create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 2.1 years ago by ▴ 10 • written 3.2 years ago by ▴ 10
0
votes
1
reply
668
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
2.2 years ago • updated 2.1 years ago slcno • 0
0
votes
1
reply
1.2k
views
igraph clustering for gene coexpression network
igraph network gene corexpression rna-seq
updated 2.1 years ago by 48k • written 4.5 years ago by • 0
0
votes
5
replies
862
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
2.1 years ago bioinformatic_trainee ▴ 10
0
votes
0
replies
628
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
2.2 years ago lianov • 0
3
votes
5
replies
1.9k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 2.3 years ago by 40k • written 2.3 years ago by ▴ 60
1
vote
1
reply
1.3k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 2.3 years ago by ★ 1.0k • written 2.3 years ago by ▴ 20
0
votes
1
reply
968
views
Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 2.3 years ago by 3.8k • written 2.3 years ago by • 0
2
votes
3
replies
909
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 2.3 years ago by 48k • written 2.3 years ago by • 0
3
votes
4
replies
784
views
need help regarding differential expression analysis
rna-seq
updated 2.3 years ago by 3.8k • written 2.3 years ago by ▴ 20
0
votes
0
replies
682
views
Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
2.3 years ago rbrns • 0
3
votes
4
replies
1.1k
views
Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
2.4 years ago Antonio M. • 0
1
vote
4
replies
3.1k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 2.4 years ago by ★ 1.0k • written 6.0 years ago by • 0
1
vote
2
replies
809
views
multifactorial design matrix
designmatrix RNA-seq limma
updated 2.5 years ago by 48k • written 2.5 years ago by ▴ 20
1
vote
7
replies
1.1k
views
how to make a contrast of uniquely DE genes
edgeR limma RNA-seq DEGseq
2.5 years ago decppced • 0
1
vote
3
replies
646
views
Questions regarding DESeq2 experimental setup and lfcShrink
DESeq2 RNA-seq
updated 2.5 years ago by 40k • written 2.5 years ago by • 0
3
votes
6
replies
2.3k
views
DESeq2: When to split multiple group samples for 'more' accurate sizefactors, dispersions etc.
Dispersion RNA-seq DESeq2 Multiple-group
updated 2.6 years ago by 40k • written 2.9 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Sorry for missing that one too. When writting blocks to an HDF5 file, the `write_block()` method for HDF5RealizationSink or TENxRealizatio…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Hi Koki, sorry for not seeing this before. > will SparseArraySeed in DelayedArray be replaced by this new sparse array format? Yes it wil…
Comment: Manual creation of qPCRset does not work by Ed Siefker ▴ 230
Thanks! This works for me.
Answer: Manual creation of qPCRset does not work by James W. MacDonald 63k
``` > mat <- matrix(rnorm(6*96), ncol = 6, nrow = 96, byrow = FALSE) > pd <- new("AnnotatedDataFrame", data = data.frame(1:6, row.names …
Answer: ukb Chromosomal position information was converted into SNPS by James W. MacDonald 63k
In my work, we almost always convert RSIDs to chr:pos because the former is ambiguous and changing whereas the latter is not. Which is like…
Votes
Answer: Manual creation of qPCRset does not work
Answer: MDS plot edgeR
A: legend with gradient in ComplexHeatmap
Comment: comparing contrasts in edger/lima using makeContrasts function
Answer: comparing contrasts in edger/lima using makeContrasts function
Awards • All
Popular Question to komal.rathi ▴ 110
Popular Question to Levi Waldron 1.1k
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Popular Question to Ed Siefker ▴ 230
Popular Question to James W. MacDonald 63k
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