Showing : rnaseq • reset
10
votes
10
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1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 1 day ago by ▴ 220 • written 6.7 years ago by ▴ 80
1
vote
3
replies
224
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 2 days ago by 50k • written 4 days ago by • 0
5
votes
3
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304
views
Log-cpm values from limma
limma edgeR RNASeq
updated 7 days ago by 50k • written 29 days ago by • 0
0
votes
3
replies
218
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 15 days ago by ★ 4.1k • written 16 days ago by • 0
0
votes
2
replies
190
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 25 days ago by • 0
0
votes
1
reply
165
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 23 days ago by 42k • written 23 days ago by • 0
1
vote
3
replies
888
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 23 days ago by ★ 1.2k • written 14 months ago by ▴ 10
0
votes
2
replies
237
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
28 days ago • updated 25 days ago catv • 0
0
votes
1
reply
124
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 29 days ago by 42k • written 29 days ago by • 0
0
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2
replies
951
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 4 weeks ago by • 0 • written 18 months ago by • 0
0
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1
reply
154
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 5 weeks ago by ★ 4.1k • written 5 weeks ago by • 0
0
votes
5
replies
1.8k
views
EdgeR: paired samples together with independant samples
RNASeq edgeR RNASeq edgeR
updated 6 weeks ago by 50k • written 11.5 years ago by ▴ 30
0
votes
2
replies
710
views
biomart not ound some prevous release
biomart rnaseq
written 5.2 years ago by ▴ 40
4
votes
16
replies
7.4k
views
Normalised counts from RUVg in RUVSeq
RUVg ruvseq rnaseq
updated 8 weeks ago by • 0 • written 9.0 years ago by ▴ 150
0
votes
2
replies
265
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
8 weeks ago kcarey • 0
0
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5
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9.3k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 8 weeks ago by • 0 • written 7.6 years ago by • 0
0
votes
2
replies
313
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
9 weeks ago kcarey • 0
2
votes
2
replies
288
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
9 weeks ago Sabiha ▴ 20
0
votes
2
replies
1.3k
views
Should immunoglobulin genes be filtered out during RNA-seq differential expression analysis
RNASeq
updated 9 weeks ago by • 0 • written 2.7 years ago by • 0
1
vote
4
replies
326
views
DESeq2 Replicates
DESeq2 RNASeq
10 weeks ago kcarey • 0
1
vote
3
replies
386
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 10 weeks ago by ★ 1.4k • written 11 weeks ago by ▴ 10
0
votes
3
replies
543
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 4 months ago by • 0
3
votes
5
replies
667
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 10 weeks ago by 42k • written 12 weeks ago by ▴ 10
0
votes
4
replies
322
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
11 weeks ago mperalc • 0
2
votes
5
replies
1.4k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 14 months ago by • 0
0
votes
2
replies
345
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
2
votes
1
reply
277
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 11 weeks ago by 42k • written 11 weeks ago by ▴ 10
3
votes
6
replies
585
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
12 weeks ago boczniak767 ▴ 720
0
votes
0
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242
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
3 months ago Abril • 0
4
votes
6
replies
640
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 3 months ago by 50k • written 4 months ago by • 0
2
votes
2
replies
437
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
3 months ago jackafiore • 0
1
vote
2
replies
1.2k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
0
votes
4
replies
439
views
Ballgown error in scan for c.tab files
ballgown RNASeq
3 months ago candacenewcome • 0
1
vote
3
replies
358
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
3 months ago island • 0
1
vote
3
replies
620
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 3 months ago by • 0
0
votes
1
reply
254
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 3 months ago by ▴ 210 • written 3 months ago by • 0
2
votes
4
replies
645
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
5
votes
7
replies
10k
views
threshold to filter lowly expressed genes
edger rnaseq
updated 4 months ago by • 0 • written 7.2 years ago by • 0
3
votes
1
reply
327
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 4 months ago by 50k • written 4 months ago by • 0
5
votes
7
replies
1.1k
views
different number of DEG because of outliers
DESeq2 RNASeq
updated 4 months ago by 50k • written 14 months ago by • 0
0
votes
1
reply
286
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
4 months ago WS • 0
3
votes
1
reply
1.7k
views
Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR RnaSeqSampleSizeData RNAseq
updated 4 months ago by 50k • written 3.0 years ago by ▴ 60
2
votes
3
replies
1.3k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 4 months ago by ★ 1.4k • written 5 months ago by • 0
1
vote
2
replies
493
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
5
votes
8
replies
3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 7.2 years ago by ▴ 40
0
votes
2
replies
1.4k
views
Conducting pair-wise comparison in DESeq2?
DESeq2 deseq2 biocondu Bioconductor RNASeq
written 15 months ago by • 0
1
vote
8
replies
2.6k
views
How to remove X & Y chromosome genes from RNAseq data
DESeq2 RNASeq
updated 5 months ago by • 0 • written 3.4 years ago by ▴ 10
1
vote
7
replies
875
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 5 months ago by 50k • written 7 months ago by • 0
1
vote
2
replies
468
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
5 months ago drewhaydensteele • 0
4
votes
4
replies
2.1k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 5 months ago by 50k • written 2.4 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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