Showing : rnaseq • reset
0
votes
4
replies
52
views
Best practice for quantifying sncRNA
Salmon sncRNA RNASeq
14 hours ago • updated 2 hours ago Abhishek • 0
5
votes
9
replies
121
views
Time series DE gene analysis with edgeR where specific timepoints have NA levels across different patients
edgeR RNASeq DifferentialExpression TimeCourse
updated 14 hours ago by 57k • written 1 day ago by ▴ 780
2
votes
6
replies
135
views
How can I use geom_label_repel with EnhancedVolcano?
ggrepel RNASeq R EnhancedVolcano
5 days ago • updated 1 day ago Loren ▴ 10
1
vote
3
replies
91
views
Issues with scaling down enrichplot's dotplot and gseaplot2 plots
RNASeq clusterProfiler enrichplot
8 days ago • updated 7 days ago jiro.becker • 0
0
votes
2
replies
1.4k
views
DESeq2 counts distribution across both genes and samples
deseq2 rnaseq
updated 9 days ago by • 0 • written 4.9 years ago by ▴ 40
3
votes
4
replies
129
views
DRIMSeq: many NAs in results compared to DESeq2 ?
DESeq2 DRIMSeq dtu RNASeq
11 days ago • updated 8 days ago sbcn ▴ 70
0
votes
1
reply
66
views
Pseudoalignment for repetitive sequences
Kallisto RNASeq pseudoaligners ShortTandemRepeats
updated 15 days ago by 57k • written 16 days ago by • 0
1
vote
3
replies
135
views
subset a list based on table
edgeR RNASeq resfilt
updated 22 days ago by ▴ 700 • written 23 days ago by • 0
2
votes
9
replies
356
views
extract fold change of a list of gene from EdgeR?
EdgeR RNAseq Foldchange
updated 21 days ago by ▴ 800 • written 25 days ago by • 0
2
votes
3
replies
143
views
DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 13 days ago by 33k • written 28 days ago by • 0
2
votes
1
reply
153
views
estimateSizeFactors before or after removing non-coding genes and filtering for low counts
DESeq2 RNASeq
updated 27 days ago by 33k • written 29 days ago by • 0
0
votes
1
reply
77
views
EnhancedVolcano Label Question
RNASeq EnhancedVolcano DEGs
updated 4 weeks ago by 3.2k • written 4 weeks ago by • 0
2
votes
1
reply
101
views
Complex design with paired and unpaired samples with edgeR RNA-seq DE analysis
edgeR RNASeq
updated 4 weeks ago by 43k • written 5 weeks ago by ▴ 150
0
votes
1
reply
131
views
Creating the correct model to account for paired-samples (patient-effect) help needed!
edgeR limma rnaseq
updated 5 weeks ago by 33k • written 5 weeks ago by • 0
1
vote
1
reply
125
views
DESeq2 for allele-specific expression with contrasts between conditions
DESeq2 AllelicImbalance edgeR RNASeq
updated 5 weeks ago by 33k • written 5 weeks ago by • 0
0
votes
8
replies
290
views
DESeq2: Variable Importance
DESeq2 RNASeq
updated 6 weeks ago by 33k • written 6 weeks ago by • 0
2
votes
3
replies
135
views
RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2 RNASeq BatchEffect limma
updated 6 weeks ago by • 0 • written 6 weeks ago by • 0
0
votes
1
reply
107
views
Query regarding WGCNA module formation
WGCNA RNAseq RNASeqData
updated 7 weeks ago by ▴ 650 • written 7 weeks ago by • 0
0
votes
0
replies
52
views
TCSeq input information
time RNAseq TCSeq
8 weeks ago curiousmind007 • 0
1
vote
5
replies
1.1k
views
Error in stattest function
R rnaseq Ballgown
updated 8 weeks ago by • 0 • written 3.5 years ago by • 0
0
votes
1
reply
79
views
Filtering DESeq2 results for | LFC | > 1 genes
RNAseq LFC DEseq
8 weeks ago ayy2110 • 0
4
votes
8
replies
327
views
Interpreting ellipses in PCAtools for bulk RNAseq
ellipse RNAseq PCAtools
written 9 weeks ago by • 0
0
votes
2
replies
157
views
Can't install KEGGprofile
KEGG RNASeq
updated 8 weeks ago by 57k • written 8 weeks ago by • 0
0
votes
1
reply
108
views
Error in DESeqDataSetFromMatrix()
DESeq2 RNAseq
updated 8 weeks ago by 33k • written 9 weeks ago by • 0
0
votes
1
reply
101
views
Extracting Go-enrichment and pathway analysis from phytozome annotation file
RNASeq GO
updated 9 weeks ago by 57k • written 9 weeks ago by • 0
0
votes
1
reply
125
views
Multi-factor Analysis in DeSEQ2
tximport R tximportData RNASeq DESeq2
updated 9 weeks ago by 33k • written 9 weeks ago by • 0
2
votes
1
reply
163
views
Salmon and DEseq2 - analysis of libraries saturated with ncRNAs
RNASeq Salmon DESeq2
updated 9 weeks ago by 33k • written 10 weeks ago by • 0
6
votes
6
replies
209
views
Weird output of biomaRt R package querying Ensembl IDs (hg19/grch37) to retrieve gene symbols
biomaRt annnotation RNASeq AnnotationDbi
9 weeks ago svlachavas ▴ 780
1
vote
2
replies
139
views
Different P-Adjusted Values In DESeq2 for the same comparaison
RNASeq DESeq2
9 weeks ago fernandogs97 • 0
0
votes
4
replies
148
views
DESeq2 Multi-factor design not full rank
RNASeq DESeq2
10 weeks ago jehimi • 0
0
votes
2
replies
147
views
Technical reps
RNASeq DESeq2
updated 10 weeks ago by ▴ 700 • written 10 weeks ago by • 0
3
votes
4
replies
258
views
LOC gene IDs for characterised genes in annotation files
Annotation RNAseq
10 weeks ago Chris • 0
0
votes
3
replies
156
views
DESeq2 ashr with and without reflevels generate different log2FoldChanges
DESeq2 RNASeq
updated 10 weeks ago by 33k • written 11 weeks ago by ▴ 10
1
vote
4
replies
248
views
Need help in running GO analysis
RNASeq R
11 weeks ago Rishav ▴ 20
2
votes
2
replies
179
views
Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR RnaSeqSampleSizeData RNAseq
updated 12 weeks ago by 43k • written 12 weeks ago by ▴ 20
0
votes
4
replies
205
views
subtracting or normalizing RNAseq reads when samples have contaminating reads
Normalization RNASeq contamination edgeR DESeq2
12 weeks ago Yuqia • 0
1
vote
6
replies
286
views
The correlation between normalized counts and TPM based on 2-factor analysis by DESeq2
DESeq2 RNASeq
3 months ago hequn • 0
1
vote
3
replies
252
views
Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData RNASeq RNASeqR
3 months ago dantasezequiel1 • 0
2
votes
2
replies
178
views
How do I set up a contrast matrix in edgeR with makeContrasts, when a relevant level was dropped?
edgeR RNASeq
updated 3 months ago by 43k • written 3 months ago by • 0
1
vote
2
replies
157
views
Unable to use ensembldb's "ensDbFromGff()" function on .gff file from NCBI
ensembldb RNASeq
3 months ago Torkel • 0
3
votes
4
replies
254
views
GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
3 months ago hgalmoore • 0
0
votes
1
reply
178
views
Limma Voom Design and Contrast Matrix- Can my parameter also be a factor?
RNASeqRData limma RNASeq RNASeqR
updated 3 months ago by 43k • written 3 months ago by • 0
0
votes
2
replies
183
views
voom-limma workflow for RNAseq samples with very different numbers of counts
voom limma RNASeq
4 months ago • updated 3 months ago annadv • 0
1
vote
3
replies
255
views
DEGpatterns and functional analysis of clusters
DESeq2 RNASeq DEGreport
updated 4 months ago by 3.2k • written 4 months ago by • 0
0
votes
2
replies
198
views
edgeR - Chapter 4.8 Time Course RNAseq experiments
edgeR TimeCourse RNASeq
updated 4 months ago by 43k • written 4 months ago by ▴ 10
0
votes
1
reply
106
views
How to analyze ribosome profiling data in the form of a 2x2x2 experiment using DESeq2
DESeq2 RiboSeq RNASeq
updated 4 months ago by 33k • written 4 months ago by • 0
0
votes
3
replies
221
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 4 months ago by 3.2k • written 4 months ago by • 0
1
vote
1
reply
164
views
read nanopore Fastq file
NanoporeRNASeq RNASeq
updated 4 months ago by 57k • written 4 months ago by • 0
4
votes
9
replies
497
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR SpikeIn RNASeq
4 months ago robert.chen • 0
2
votes
2
replies
189
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
5 months ago • updated 4 months ago n.tear ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2 question: why I got discrepancy results for DEGs when using different way by Michael Love 33k
Q1: No I meant just use your results from above that you called "the first way". Not sub-setting, as you will have worse dispersion estimat…
Comment: Best practice for quantifying sncRNA by Abhishek • 0
I wonder what would be a good metric to assess the quantification quality
Comment: Best practice for quantifying sncRNA by Abhishek • 0
Thank you for sharing your thoughts. I used Salmon and indexed using hg38 gencodes transcriptome. After the tximport step, I ended up gett…
Comment: DESeq2 question: why I got discrepancy results for DEGs when using different way by Ming ▴ 350
Thx so much for the diagnosis and advice. Indeed, in my data, some genes have all 0 for all sampes of a contrast for both "Mut" and "WT" gr…
Comment: Best practice for quantifying sncRNA by Steve Lianoglou 13k
> It's my opinion that miRNA is a mirage intended to make MDs salivate and biostatisticians wail in misery, but what do I know? I'll tell …
Votes
Comment: Idea: Using DESeq2 to test a change in ratio of two genes
Time Series Analysis
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels
Answer: Time series DE gene analysis with edgeR where specific timepoints have NA levels
Awards • All
Popular Question to amalthomas111 • 0
Scholar to gabriel.hoffman ▴ 90
Popular Question to Thomas Maurel ▴ 790
Scholar to James W. MacDonald 57k
Teacher to Guido Hooiveld ★ 3.0k
Locations • All
Australia, 12 minutes ago
United States, 17 minutes ago
United States, 25 minutes ago
The city by the bay, 1 hour ago
Republic of Ireland, 2 hours ago
Traffic: 872 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6