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138
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Can you find the correct transcript in scRNA seq data
scRNAseq
RNAseq
updated 24 days ago by
ATpoint
★ 4.1k • written 25 days ago by
Merav
• 0
0
votes
1
reply
160
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 24 days ago by
Michael Love
41k • written 24 days ago by
Adelaide
• 0
0
votes
2
replies
295
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
4 weeks ago • updated 28 days ago
fer_talavera
• 0
0
votes
2
replies
129
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
15 days ago
prity6459
• 0
0
votes
1
reply
174
views
DESeq2 gives an error and R crashes
DESeq2
23 days ago • updated 22 days ago
Shefali
• 0
0
votes
7
replies
692
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
9 weeks ago • updated 10 days ago
shepherl
3.9k
0
votes
0
replies
117
views
Warning while loading DEP package
DEP
updated 15 days ago by
shepherl
3.9k • written 15 days ago by
Namrata
• 0
0
votes
1
reply
81
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
z_bahari
• 0
0
votes
0
replies
82
views
News:
Important Release 3.18 Freeze Announcment
Release
release
Bioconductor
Bioconducto
22 days ago
shepherl
3.9k
0
votes
1
reply
49
views
package goseq seems to be not available on the latest version of R
goseq
updated 14 hours ago by
Gordon Smyth
50k • written 18 hours ago by
Patrycja
• 0
0
votes
0
replies
36
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
1 day ago
yvonneh
• 0
0
votes
3
replies
157
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 3 days ago by
Alejandro Reyes
★ 1.9k • written 16 days ago by
Alessia
• 0
0
votes
0
replies
78
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
9 days ago • updated 5 days ago
Sara
• 0
0
votes
1
reply
40
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 2 days ago by
4r-rtg
• 0
0
votes
1
reply
93
views
putting my own expression data in deseq2
DESeq2
updated 4 days ago by
ATpoint
★ 4.1k • written 4 days ago by
Dev
• 0
0
votes
0
replies
80
views
Enzyme Engineering
BioTIP
17 days ago
bocchemistry
• 0
0
votes
0
replies
70
views
Empty table plot using plotGseaTable()
fgsea
2 days ago • updated 17 hours ago
Chris
• 0
0
votes
1
reply
119
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 2 days ago by
ATpoint
★ 4.1k • written 2 days ago by
angelathuynh5
• 0
0
votes
4
replies
240
views
Minfi - estimatecellscount
min
minfi
updated 5 days ago by
James W. MacDonald
65k • written 5 weeks ago by
clacarion
• 0
0
votes
1
reply
162
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 28 days ago by
Gordon Smyth
50k • written 28 days ago by
avery
• 0
0
votes
4
replies
220
views
Storing directories inside an ExperimentHub package?
ExperimentHub
23 days ago • updated 22 days ago
Tim Barry
• 0
0
votes
7
replies
413
views
DESeq filtering specific to contrasts
DESeq2
updated 14 days ago by
Michael Love
41k • written 11 weeks ago by
Emma
• 0
0
votes
1
reply
140
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 18 days ago by
kamryncole1963
• 0 • written 23 days ago by
Sara
• 0
0
votes
3
replies
133
views
Store output of matchPWM()
biostrings
Biostrings
updated 2 days ago by
James W. MacDonald
65k • written 2 days ago by
mat149
▴ 70
0
votes
1
reply
70
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 4 days ago by
shepherl
3.9k • written 4 days ago by
bounlu
• 0
0
votes
1
reply
92
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 4 days ago by
Michael Love
41k • written 4 days ago by
Agung
• 0
0
votes
3
replies
203
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 18 days ago by
Michael Love
41k • written 19 days ago by
andrebolerbarros
▴ 20
0
votes
4
replies
235
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
16 days ago • updated 14 days ago
lonn
• 0
0
votes
1
reply
1.3k
views
Tutorial:
Online workshop "Working with ChatGPT in R" 2023-03-09
chatgpt
programming
updated 21 days ago by
gptnederlands.nl
• 0 • written 14 months ago by
Wolfgang Huber
★ 13k
0
votes
2
replies
241
views
Regressing out batch effects
DESeq2
updated 24 days ago by
Michael Love
41k • written 29 days ago by
kys91240
• 0
0
votes
1
reply
132
views
Bioinformatics student
Des
DESeq2
updated 21 days ago by
hemantcnaik
• 0 • written 21 days ago by
Sahar
• 0
0
votes
1
reply
142
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 16 days ago by
ATpoint
★ 4.1k • written 17 days ago by
quanah.hudson
• 0
0
votes
1
reply
123
views
ATACseq merge peaks
DiffBind
updated 8 days ago by
ATpoint
★ 4.1k • written 9 days ago by
Shloka
• 0
0
votes
2
replies
153
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 11 days ago by
taur.vil
• 0
0
votes
3
replies
110
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 2 days ago by
ATpoint
★ 4.1k • written 2 days ago by
james.zhang20
• 0
0
votes
1
reply
705
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 21 days ago by
President Gamer
• 0 • written 11 months ago by
abhisek001
• 0
0
votes
4
replies
191
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
15 days ago
sropri
• 0
0
votes
1
reply
130
views
Deseq2 Rlog transformation
DESeq2
updated 19 days ago by
ATpoint
★ 4.1k • written 20 days ago by
Sahar
• 0
0
votes
0
replies
51
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
4 days ago
Maria Doyle
▴ 70
0
votes
2
replies
74
views
DESeq2 v1.35.0
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
Espresso
• 0
0
votes
6
replies
152
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 8 hours ago by
swbarnes2
★ 1.3k • written 1 day ago by
arfranco
▴ 130
0
votes
0
replies
29
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
1 day ago
Ian D.
▴ 70
0
votes
1
reply
214
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 3 days ago by
James W. MacDonald
65k • written 4 days ago by
SSSJec
• 0
0
votes
1
reply
128
views
Granges regionCounts not returning the expected number of entries
methylKit
29 days ago • updated 28 days ago
Modoc Kesner
▴ 10
0
votes
0
replies
78
views
News:
TIDES USA 2024
flowBeads
17 days ago
bocsci11
• 0
0
votes
0
replies
91
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
22 days ago
Stevie Pederson
• 0
0
votes
4
replies
261
views
DEG with low counts
DESeq2
updated 15 days ago by
Michael Love
41k • written 19 days ago by
Rajat
• 0
0
votes
2
replies
108
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
4 days ago • updated 1 day ago
Aurora
• 0
0
votes
5
replies
291
views
Error for AnnotationForge makeOrgPackageFromNCBI function
OrgDb
AnnotationForge
updated 10 days ago by
James W. MacDonald
65k • written 12 days ago by
Gayatri
• 0
0
votes
0
replies
94
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
18 days ago
Virangika
• 0
201 results • Page
3 of 5
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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