Showing : RNA-SEQ • reset
9
votes
12
replies
7.7k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 1 day ago by • 0 • written 8.8 years ago by ▴ 30
3
votes
3
replies
267
views
permutation test in edgeR
rna-seq edgeR
updated 5 days ago by 50k • written 12 days ago by • 0
0
votes
1
reply
895
views
Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 4 months ago by ★ 4.0k • written 6.0 years ago by • 0
0
votes
2
replies
298
views
WGCNA less samples
RNA-Seq WGCNA Worms
4 months ago davca • 0
0
votes
4
replies
667
views
DESeq2 : standardising variation between treatments
RNA-seq DESeq2
6 months ago ar14g12 • 0
0
votes
2
replies
3.5k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 3.8 years ago by ▴ 80
2
votes
3
replies
1.5k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 7 months ago by 50k • written 7 months ago by • 0
0
votes
3
replies
634
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 7 months ago by ★ 1.9k • written 7 months ago by • 0
0
votes
2
replies
2.2k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 7 months ago by • 0 • written 2.0 years ago by • 0
3
votes
4
replies
841
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
8 months ago Eva ▴ 10
0
votes
10
replies
2.2k
views
Error in reading data on isoformswitchanalyzeR
isoformswitchanalyzeR rna-seq splice-variants
written 5.1 years ago by • 0
0
votes
3
replies
662
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 10 months ago by 41k • written 10 months ago by • 0
5
votes
7
replies
1.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 10 months ago by 50k • written 10 months ago by ▴ 10
0
votes
2
replies
1.2k
views
Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 11 months ago by • 0 • written 3.5 years ago by • 0
0
votes
3
replies
832
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 11 months ago by 65k • written 11 months ago by • 0
0
votes
3
replies
694
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 11 months ago by 65k • written 11 months ago by • 0
1
vote
1
reply
1.3k
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 12 months ago by ★ 4.0k • written 12 months ago by • 0
0
votes
1
reply
662
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 12 months ago by 65k • written 12 months ago by • 0
2
votes
2
replies
704
views
Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 13 months ago by ★ 4.0k • written 13 months ago by • 0
0
votes
1
reply
634
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
14 months ago Jenny Drnevich ★ 2.0k
1
vote
4
replies
985
views
Nested paired design with covariates in limma
RNA-seq Nested paired design limma
updated 14 months ago by 50k • written 4.1 years ago by • 0
4
votes
8
replies
2.1k
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
updated 14 months ago by 65k • written 3.9 years ago by ▴ 30
0
votes
1
reply
688
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 16 months ago by 41k • written 17 months ago by • 0
4
votes
6
replies
6.0k
views
strange results with featureCounts
RNA-seq featureCounts total RNA
updated 18 months ago by ▴ 20 • written 5.9 years ago by ▴ 10
5
votes
9
replies
1.8k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
21 months ago Yang Shi ▴ 10
2
votes
2
replies
1.2k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
21 months ago Yang Shi ▴ 10
0
votes
0
replies
844
views
Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
21 months ago eolson • 0
2
votes
2
replies
954
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 21 months ago by 50k • written 21 months ago by • 0
3
votes
2
replies
5.0k
views
Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
updated 23 months ago by ▴ 10 • written 3.7 years ago by ▴ 80
5
votes
5
replies
1.6k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
2.1 years ago • updated 23 months ago 9906201a ▴ 20
3
votes
3
replies
3.3k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 2.1 years ago by ▴ 30 • written 5.2 years ago by ▴ 30
0
votes
2
replies
3.6k
views
Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage gage package pathview rna-seq
updated 2.1 years ago by • 0 • written 6.2 years ago by • 0
1
vote
5
replies
1.9k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.2 years ago Lucy ▴ 60
1
vote
3
replies
1.4k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 2.2 years ago by 41k • written 2.2 years ago by • 0
5
votes
2
replies
21k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
updated 2.2 years ago by • 0 • written 5.3 years ago by ▴ 30
0
votes
5
replies
3.5k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.3 years ago by ★ 4.0k • written 3.1 years ago by • 0
0
votes
1
reply
881
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 2.3 years ago by 50k • written 2.3 years ago by • 0
0
votes
7
replies
2.4k
views
Error reading kallisto files using tximport for cross species RNA-Seq analysis
kallisto tximport RNA-Seq across species
updated 2.5 years ago by • 0 • written 6.9 years ago by ▴ 40
5
votes
12
replies
5.5k
views
DESeq2 time series contrasts between timepoints
rna-seq deseq2
updated 2.5 years ago by ▴ 30 • written 6.6 years ago by ▴ 40
1
vote
1
reply
2.6k
views
create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 2.7 years ago by ▴ 10 • written 3.8 years ago by ▴ 10
0
votes
1
reply
990
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
2.7 years ago slcno • 0
0
votes
1
reply
1.5k
views
igraph clustering for gene coexpression network
igraph network gene corexpression rna-seq
updated 2.7 years ago by 50k • written 5.1 years ago by • 0
0
votes
5
replies
1.2k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
2.7 years ago bioinformatic_trainee ▴ 10
0
votes
0
replies
893
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
2.7 years ago lianov • 0
3
votes
5
replies
2.5k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 2.8 years ago by 41k • written 2.8 years ago by ▴ 60
1
vote
1
reply
1.7k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 2.9 years ago by ★ 1.0k • written 2.9 years ago by ▴ 20
0
votes
1
reply
1.5k
views
Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
2
votes
3
replies
1.2k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 2.9 years ago by 50k • written 2.9 years ago by • 0
3
votes
4
replies
1.1k
views
need help regarding differential expression analysis
rna-seq
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by ▴ 20
0
votes
0
replies
923
views
Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
2.9 years ago rbrns • 0
50 results • Page 1 of 1
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Thanks Robert!
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Votes
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
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