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Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
1 hour ago
4r-rtg
• 0
0
votes
1
reply
51
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 11 hours ago by
Rory Stark
★ 5.2k • written 1 day ago by
Ian D.
▴ 70
0
votes
1
reply
27
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
updated 1 hour ago by
ATpoint
★ 4.1k • written 12 hours ago by
kcarey
• 0
0
votes
3
replies
51
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 51 minutes ago by
ATpoint
★ 4.1k • written 12 hours ago by
james.zhang20
• 0
0
votes
1
reply
89
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 14 hours ago by
ATpoint
★ 4.1k • written 14 hours ago by
angelathuynh5
• 0
2
votes
0
replies
29
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
15 hours ago
shepherl
3.8k
0
votes
0
replies
46
views
Empty table plot using plotGseaTable()
fgsea
16 hours ago • updated 14 hours ago
Chris
• 0
0
votes
3
replies
96
views
Store output of matchPWM()
biostrings
Biostrings
updated 16 hours ago by
James W. MacDonald
65k • written 19 hours ago by
mat149
▴ 70
0
votes
3
replies
202
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 14 hours ago by
Michael Love
41k • written 1 day ago by
HAK
• 0
0
votes
2
replies
110
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
1 day ago • updated 10 hours ago
Yveto
• 0
8
votes
6
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 1 day ago by
Leonard Goldstein
▴ 200 • written 6.7 years ago by
Sylvain Foisy
▴ 80
0
votes
1
reply
198
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 1 day ago by
James W. MacDonald
65k • written 2 days ago by
SSSJec
• 0
3
votes
4
replies
161
views
Help with error using camera() in limma
CAMERA
limma
1 day ago
Chris
• 0
1
vote
1
reply
75
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
marcusn
• 0
0
votes
1
reply
66
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
updated 1 day ago by
Michael Love
41k • written 2 days ago by
Aurora
• 0
0
votes
1
reply
80
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
Agung
• 0
0
votes
0
replies
41
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
1 day ago
Maria Doyle
▴ 70
0
votes
1
reply
54
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 1 day ago by
shepherl
3.8k • written 2 days ago by
bounlu
• 0
0
votes
1
reply
75
views
putting my own expression data in deseq2
DESeq2
updated 2 days ago by
ATpoint
★ 4.1k • written 2 days ago by
Dev
• 0
2
votes
2
replies
161
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
2 days ago
Chris
• 0
0
votes
3
replies
200
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 1 day ago by
James W. MacDonald
65k • written 2 days ago by
SSSJec
• 0
0
votes
0
replies
50
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
2 days ago
Chris
• 0
3
votes
3
replies
191
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 3 days ago by
ATpoint
★ 4.1k • written 3 days ago by
bioinf
▴ 10
1
vote
1
reply
106
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 5 days ago by
Leo Lahti
▴ 40 • written 5 days ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
179
views
PCA plot suggestions
DESeq2
PCAtools
updated 5 days ago by
Michael Love
41k • written 7 days ago by
Aaliya
• 0
1
vote
3
replies
184
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 5 days ago by
Michael Love
41k • written 6 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
110
views
ATACseq merge peaks
DiffBind
updated 5 days ago by
ATpoint
★ 4.1k • written 7 days ago by
Shloka
• 0
1
vote
1
reply
147
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 6 days ago by
Gordon Smyth
50k • written 10 days ago by
Lluís Revilla Sancho
▴ 730
1
vote
7
replies
283
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
6 days ago • updated 5 days ago
pl23
• 0
2
votes
9
replies
338
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 6 days ago by
James W. MacDonald
65k • written 6 days ago by
Alexandre
• 0
0
votes
0
replies
67
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
7 days ago • updated 3 days ago
Sara
• 0
2
votes
5
replies
212
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 6 days ago by
James W. MacDonald
65k • written 8 days ago by
bandconductor
• 0
1
vote
4
replies
297
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
8 days ago • updated 6 days ago
winwater0928
• 0
0
votes
2
replies
139
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 9 days ago by
taur.vil
• 0
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
11 days ago • updated 16 hours ago
Chris
• 0
0
votes
3
replies
152
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 1 day ago by
Alejandro Reyes
★ 1.9k • written 14 days ago by
Alessia
• 0
1
vote
2
replies
689
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
14 days ago • updated 5 days ago
ussarizona
▴ 10
15
votes
23
replies
1.9k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
4 weeks ago • updated 1 day ago
Chris
• 0
0
votes
4
replies
237
views
Minfi - estimatecellscount
min
minfi
updated 2 days ago by
James W. MacDonald
65k • written 4 weeks ago by
clacarion
• 0
1
vote
4
replies
444
views
DEseq2 coefficient
DESeq2
coefficient
9 weeks ago • updated 16 hours ago
JKim
• 0
6
votes
19
replies
2.4k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 1 day ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
2
votes
2
replies
1.0k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 1 day ago by
XW
• 0 • written 7.9 years ago by
tati6406
• 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 1 day ago by
XW
• 0 • written 13.0 years ago by
Babara Mueller
▴ 10
43 results • Page
1 of 1
Recent ...
Replies
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq
by
james.zhang20
• 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Comment: Deseq2 and Normalization of RNA sequencing data
by
ATpoint
★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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