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2
replies
172
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
21 days ago • updated 18 days ago
Aurora
• 0
0
votes
0
replies
144
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools
TCGA
26 days ago • updated 18 days ago
glaciya2018
• 0
0
votes
2
replies
217
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
19 days ago • updated 18 days ago
kcarey
• 0
0
votes
1
reply
180
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 18 days ago by
Gordon Smyth
50k • written 18 days ago by
z_bahari
• 0
0
votes
1
reply
164
views
Gene-by-sample covariates in limma
Metabolomics
limma
updated 18 days ago by
Gordon Smyth
50k • written 18 days ago by
c53aba27
• 0
0
votes
0
replies
100
views
flowStats for CyTOF
flowStats
18 days ago
tholmes
• 0
0
votes
2
replies
175
views
DESeq2 v1.35.0
DESeq2
updated 18 days ago by
Michael Love
42k • written 18 days ago by
Espresso
• 0
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 18 days ago by
James W. MacDonald
66k • written 2.4 years ago by
yanchangjian2019
• 0
0
votes
0
replies
97
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
18 days ago
yvonneh
• 0
0
votes
0
replies
89
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
18 days ago
Ian D.
▴ 70
0
votes
1
reply
143
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 19 days ago by
4r-rtg
• 0
0
votes
3
replies
230
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 18 days ago by
ATpoint
★ 4.1k • written 19 days ago by
james.zhang20
• 0
0
votes
2
replies
192
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 28 days ago by
taur.vil
• 0
1
vote
2
replies
295
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
20 days ago • updated 19 days ago
Yveto
• 0
0
votes
3
replies
305
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 19 days ago by
Michael Love
42k • written 20 days ago by
HAK
• 0
4
votes
0
replies
147
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
19 days ago
shepherl
3.9k
15
votes
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
4 weeks ago • updated 19 days ago
Chris
▴ 10
1
vote
4
replies
533
views
DEseq2 coefficient
DESeq2
coefficient
12 weeks ago • updated 19 days ago
JKim
• 0
3
votes
4
replies
267
views
Help with error using camera() in limma
CAMERA
limma
20 days ago
Chris
▴ 10
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 20 days ago by
XW
• 0 • written 8.0 years ago by
tati6406
• 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 20 days ago by
XW
• 0 • written 13.1 years ago by
Babara Mueller
▴ 10
0
votes
1
reply
266
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 20 days ago by
James W. MacDonald
66k • written 21 days ago by
SSSJec
• 0
0
votes
3
replies
283
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 20 days ago by
James W. MacDonald
66k • written 21 days ago by
SSSJec
• 0
15
votes
23
replies
2.1k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
7 weeks ago • updated 20 days ago
Chris
▴ 10
6
votes
19
replies
2.6k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 20 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
0
votes
3
replies
190
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 20 days ago by
Alejandro Reyes
★ 1.9k • written 4 weeks ago by
Alessia
• 0
1
vote
1
reply
160
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 20 days ago by
Michael Love
42k • written 20 days ago by
marcusn
• 0
0
votes
1
reply
140
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 20 days ago by
Michael Love
42k • written 21 days ago by
Agung
• 0
0
votes
0
replies
96
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
20 days ago
Maria Doyle
▴ 70
0
votes
1
reply
126
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 20 days ago by
shepherl
3.9k • written 21 days ago by
bounlu
• 0
0
votes
1
reply
141
views
putting my own expression data in deseq2
DESeq2
updated 20 days ago by
ATpoint
★ 4.1k • written 21 days ago by
Dev
• 0
2
votes
2
replies
240
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
21 days ago
Chris
▴ 10
0
votes
0
replies
98
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
21 days ago
Chris
▴ 10
0
votes
4
replies
267
views
Minfi - estimatecellscount
min
minfi
updated 21 days ago by
James W. MacDonald
66k • written 7 weeks ago by
clacarion
• 0
3
votes
3
replies
275
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 22 days ago by
ATpoint
★ 4.1k • written 22 days ago by
bioinf
▴ 10
0
votes
0
replies
101
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
26 days ago • updated 22 days ago
Sara
• 0
1
vote
1
reply
155
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 24 days ago by
Leo Lahti
▴ 40 • written 24 days ago by
Dario Strbenac
★ 1.5k
1
vote
7
replies
361
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
25 days ago • updated 24 days ago
pl23
• 0
0
votes
2
replies
229
views
PCA plot suggestions
DESeq2
PCAtools
updated 24 days ago by
Michael Love
42k • written 26 days ago by
Aaliya
• 0
1
vote
2
replies
756
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 24 days ago
Patadù
▴ 10
1
vote
3
replies
257
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 24 days ago by
Michael Love
42k • written 25 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
175
views
ATACseq merge peaks
DiffBind
updated 24 days ago by
ATpoint
★ 4.1k • written 26 days ago by
Shloka
• 0
1
vote
4
replies
362
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
27 days ago • updated 25 days ago
winwater0928
• 0
2
votes
9
replies
429
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 25 days ago by
James W. MacDonald
66k • written 25 days ago by
Alexandre
• 0
2
votes
5
replies
262
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 25 days ago by
James W. MacDonald
66k • written 27 days ago by
bandconductor
• 0
1
vote
2
replies
177
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
26 days ago
ATpoint
★ 4.1k
0
votes
2
replies
268
views
featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
28 days ago • updated 26 days ago
shuwangxinze1996
• 0
0
votes
8
replies
395
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 26 days ago by
swbarnes2
★ 1.4k • written 27 days ago by
Aaliya
• 0
0
votes
1
reply
167
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 26 days ago by
Michael Love
42k • written 26 days ago by
kcarey
• 0
2
votes
13
replies
495
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
29 days ago • updated 26 days ago
fernanda.backsouza
▴ 10
170 results • Page
3 of 4
Recent ...
Replies
Comment: Ensembl plants at annotationHub?
by
Johannes Rainer
★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Comment: Errors in chromosome annotation-biomaRt
by
blackwidowzzz
• 0
I recommend using a different dataset specific to your rat genome assembly version 8. You can search for available datasets within Ensembl …
Answer: Errors in chromosome annotation-biomaRt
by
James W. MacDonald
66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat
by
James W. MacDonald
66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons
by
James W. MacDonald
66k
In that case, probably easiest to subset to the groups being compared.
Votes
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
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