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8
views
Error in msaFun Cannot open input file. No alignment!
msa
6 hours ago
Kamil Slowikowski
▴ 30
0
votes
0
replies
16
views
Help with identifying genes mapped to KEGG pathway using pathview
pathview
8 hours ago
Julie
• 0
0
votes
0
replies
14
views
Help with Complex DESeq2 Design
DESeq2
8 hours ago
kelsey.beavers
• 0
1
vote
0
replies
34
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
13 hours ago
andrebolerbarros
▴ 30
0
votes
1
reply
80
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 1 day ago by
Gordon Smyth
50k • written 3 days ago by
Gerhard Thallinger
▴ 180
0
votes
2
replies
137
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
6 days ago • updated 5 days ago
Sam
▴ 10
0
votes
1
reply
117
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks
TCGA
clinical
TCGA-BRCA
written 6 days ago by
BioinfoMug
• 0
0
votes
1
reply
108
views
Exact same results in Diffbind with different normalization methods
DiffBind
7 days ago • updated 2 days ago
red_bricks
▴ 50
0
votes
0
replies
71
views
FELLA plotGraph function won't change the legend
FELLA
7 days ago
yuhang
• 0
0
votes
0
replies
71
views
medips-output
ngsReports
MEDIPS
7 days ago
subhiksha
• 0
0
votes
0
replies
60
views
Join BOC Sciences at Drug Discovery Chemistry
alabaster.schemas
db0
7 days ago
bocsci11
• 0
0
votes
0
replies
65
views
The graphical interface of FELLA doesn't work
FELLA
7 days ago
yuhang
• 0
0
votes
0
replies
76
views
DEXSeq plot error
DEXSeq
DEXSeqNAvalues
DEXseq
7 days ago
jean-christophe.helbling
• 0
0
votes
0
replies
89
views
To analyze StringTie data using the isoformSwitchAnalyzeR package
IsoformSwitchAnalyzeR
11 days ago
Henry
• 0
0
votes
1
reply
130
views
Rcpp compilation error
Release
Rcpp
updated 10 days ago by
ATpoint
★ 3.9k • written 11 days ago by
Robert K. Bradley
▴ 40
0
votes
0
replies
89
views
Rain error: invalid annotation of time points
rain
11 days ago
mpuli011
• 0
0
votes
0
replies
78
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi
minfiDataEPIC
11 days ago
Felix
• 0
0
votes
0
replies
84
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
TCGAbiolinks
13 days ago
Giovanni Calice
▴ 160
0
votes
0
replies
94
views
Error: grouping factors must have > 1 sampled level
Mast
mastR
MAST
updated 14 days ago by
James W. MacDonald
65k • written 14 days ago by
Andrew
• 0
0
votes
0
replies
76
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts
Rsubread
14 days ago
chris2.a.white
• 0
0
votes
0
replies
96
views
Could SGSeq utilizes "ts" tag produced from minimap2 other than "XS" tag?
XS-tag
SplicedAlignment
SGSeq
minimap2
17 days ago
jk
• 0
0
votes
0
replies
104
views
Can I combine collinear variables into a single value
BatchEffect
limma
18 days ago
Harrsha
• 0
0
votes
0
replies
154
views
Error in set(x, j = name, value = value) : Supplied 52 items to be assigned to 55 items of column 'locus'. If you wish to 'recycle' the RHS please…
ASpli
18 days ago
vipul14
• 0
0
votes
0
replies
77
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R
ATACseqQC
18 days ago
danalvoronov
▴ 10
0
votes
0
replies
103
views
lfcSE
RGSEA
19 days ago
Gordon
• 0
0
votes
4
replies
193
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
20 days ago • updated 18 days ago
mperalc
• 0
1
vote
0
replies
98
views
Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k
MethylationArray
TCGAbiolinks
Tcga
TCGAbiolinksGUI.data
21 days ago
BioinfoMug
• 0
0
votes
0
replies
108
views
Unclear exon-exon connection after RSubjunc() usage
IGV
Rsubjunc
Rsubread
21 days ago
thomas.heigl.ibk
• 0
0
votes
1
reply
206
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 21 days ago by
ATpoint
★ 3.9k • written 24 days ago by
sodiogoes
• 0
0
votes
6
replies
477
views
StringDB: Cannot finish their tutorial because of an error
STRINGdb
updated 8 days ago by
qianyi13
• 0 • written 24 days ago by
Pavel
• 0
0
votes
2
replies
247
views
problem in installing the new version of bioconductor
ANCOMBC
updated 24 days ago by
shepherl
3.8k • written 25 days ago by
Maryam
• 0
0
votes
0
replies
128
views
Comparing the effects of a condition over time in two seperate tissues
MAST
26 days ago
Dillon
• 0
0
votes
4
replies
231
views
Installation problem of rtracklayer on Bioconductor version 3.19
newpackage
rtracklayer
updated 26 days ago by
shepherl
3.8k • written 26 days ago by
Lucille
• 0
0
votes
3
replies
172
views
problems updating package
TrajectoryGeometry
26 days ago
michael.shapiro
• 0
0
votes
0
replies
139
views
how to solve this error?
ChAMPdata
ChAMP
4 weeks ago
Meghana
• 0
1
vote
0
replies
153
views
FCS3.2 reading
flowWorkspace
flowCore
CytoML
4 weeks ago
jarod
▴ 30
0
votes
0
replies
118
views
flowAI: flow rare check in R vs FlowJo
flowAI
4 weeks ago • updated 28 days ago
Olena
• 0
0
votes
0
replies
141
views
ISO statistical test for obs-exp A,T,C,G counts by genomic range/position
GenomicRanges
4 weeks ago
mat149
▴ 70
0
votes
0
replies
100
views
GDC slides download
TCGAbiolinks
4 weeks ago
jain72744
• 0
0
votes
0
replies
135
views
Differential expression analysis between different species
DEG
RNASeqData
DifferentialExpression
SCBN
RNASeq
4 weeks ago
Abril
• 0
0
votes
4
replies
214
views
I need to calculate the survival rate of TCGA databases
TCGAbiolinks
Survival
updated 4 weeks ago by
Lluís Revilla Sancho
▴ 730 • written 5 weeks ago by
tirordep
• 0
0
votes
1
reply
149
views
"Counts" in enrichGO
GSEABase
updated 5 weeks ago by
Tyler Sagendorf
▴ 10 • written 5 weeks ago by
Matthew
• 0
0
votes
1
reply
159
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor
WGCNA
updated 5 weeks ago by
ATpoint
★ 3.9k • written 5 weeks ago by
Priya
• 0
2
votes
15
replies
498
views
Problems with enrichGO
clusterProfiler
enrichGO
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
cinzia.spagnoli
• 0
0
votes
0
replies
91
views
Best method for annotating distal peaks
ChIPSeq
annotation
ChIPpeakAnno
5 weeks ago
nilanjanamani88
• 0
1
vote
1
reply
171
views
502 error biomaRt getLDS()
ensembldb
biomaRt
updated 5 weeks ago by
Robin
• 0 • written 5 weeks ago by
Pez
▴ 10
0
votes
3
replies
263
views
Unable to install clusterProfiler
clusterProfiler
updated 4 weeks ago by
Perry
• 0 • written 5 weeks ago by
harsh
• 0
0
votes
0
replies
113
views
rain: Error in peakl[[x]] : subscript out of bounds
rain
5 weeks ago
mata
• 0
1
vote
5
replies
295
views
BiomaRt download data error
biomaRt
updated 5 weeks ago by
Mike Smith
★ 6.4k • written 5 weeks ago by
Max Bone
• 0
0
votes
0
replies
118
views
Recount3 error downloading data
recount3
recount
5 weeks ago
Max Bone
• 0
1,000 results • Page
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Replies
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
Comment: Unable to annotate ExpressionSet object from hugene11st chip
by
Efra
• 0
I did as you told, and after running ```eset.annot <- annotateEset(eset, hugene11sttranscriptcluster.db)``` I got the next output: ``` 'se…
Votes
C: How to check that the reads in two fastq files are in the same order
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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