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Votes
0
votes
2
replies
39
views
errors in annotation
org.Bt.eg.db
3 days ago • updated 22 minutes ago
Josie
• 0
0
votes
0
replies
10
views
How can I properly decode error when using ASICS?
ASICSdata
ASICS
3 hours ago
nep63
• 0
0
votes
1
reply
45
views
Conversion of UniProt to Ensembl
biomaRt
ensembldb
UniProt.ws
updated 4 hours ago by
James W. MacDonald
60k • written 3 days ago by
Recep
• 0
2
votes
2
replies
38
views
the difference between getGEO and getGEOSuppFiles
MicroarrayData
16 hours ago • updated 5 hours ago
Fatemeh
• 0
2
votes
6
replies
239
views
error running UniProt.ws
UniProt.ws
updated 8 hours ago by
James W. MacDonald
60k • written 5 weeks ago by
julien.wollbrett
▴ 10
0
votes
0
replies
13
views
Argument is of length zero in variancePartition/Dream
expression
variancePartition
edgeR
8 hours ago
Jonathan
• 0
0
votes
1
reply
21
views
GSEA with Wikipathways not entirely reproducible
clusterProfiler
updated 8 hours ago by
Guido Hooiveld
★ 3.3k • written 10 hours ago by
Susana
• 0
4
votes
5
replies
460
views
Pathview unable to download pathways
clusterProfiler
KEGGgraph
clusterpr
KEGG
pathview
updated 9 hours ago by
Guido Hooiveld
★ 3.3k • written 7 weeks ago by
rama
▴ 10
0
votes
2
replies
605
views
getBM error in the biomaRt R package
Annotation
updated 9 hours ago by
qiz218591
• 0 • written 8 months ago by
arungowda9738
• 0
0
votes
0
replies
10
views
Correlation between two different datasets: between results of RNAseq and absence/presence of Type3 Secretion System
RNASeq
Correlation
DESeq2
11 hours ago
keshav.prasad.gubbi
• 0
0
votes
2
replies
101
views
IsoformSwitchAnalyzeR package on mouse data
rnaseq
IsoformSwitchAnalyzeR
updated 11 hours ago by
k.vitting.seerup
▴ 120 • written 19 days ago by
Ryan
• 0
2
votes
1
reply
43
views
Error in Create switchAnalyzeRlist
AlternativeSplicing
RNASeq
IsoformSwitchAnalyzeR
gtf
updated 11 hours ago by
k.vitting.seerup
▴ 120 • written 2 days ago by
bpshtiwan
▴ 10
0
votes
1
reply
43
views
Retrieve gene summary start/end in biomart query
biomaRt
updated 12 hours ago by
Mike Smith
★ 5.7k • written 1 day ago by
rbenel
▴ 20
1
vote
2
replies
83
views
TPM normalization starting with read counts
edgeR
DESeq2
updated 15 hours ago by
Gordon Smyth
46k • written 1 day ago by
JAcky
• 0
2
votes
5
replies
1.3k
views
using DESeq2 for ATAC analyses
ATACSeq
DESeq2
updated 1 day ago by
eric.kern13
▴ 10 • written 10 months ago by
changxu.fan
▴ 10
0
votes
1
reply
36
views
Adding custom transcript to Salmon index
salmon
updated 1 day ago by
ATpoint
★ 1.4k • written 1 day ago by
Ray
• 0
0
votes
0
replies
42
views
Strange Dispersion plot
DESeq2
1 day ago
Yiqi
• 0
0
votes
1
reply
89
views
Design and contrast matrices for analyzing the effect of two factors of interest on protein expression, controlling for factors and covariates not of…
limma
Proteomics
ProteomicsWorkflow
updated 2 days ago by
Gordon Smyth
46k • written 3 days ago by
samantha.v.goncalves
• 0
0
votes
0
replies
44
views
Correlation between CpG methylation and gene expression from DESeq2-> Normalization of counts using VST + fpkm/rpkm for optimal normalization?
DESeq2
3 days ago
Brendon Herring
• 0
0
votes
2
replies
163
views
Error with TCGA package - TCGAbiolinks
TCGAbiolinks
RNASeq
CancerData
updated 3 days ago by
Tiago C. Silva
▴ 220 • written 7 weeks ago by
JAcky
• 0
0
votes
2
replies
193
views
GDCdownload Directory Problem :(
TCGAWorkflowData
TCGAbiolinks
updated 3 days ago by
Marcel Ramos
570 • written 3 months ago by
Emre
• 0
1
vote
2
replies
108
views
I want to know how to analyze TCGA data with maftools.
TCGAWorkflowData
updated 3 days ago by
Marcel Ramos
570 • written 20 days ago by
Y
• 0
1
vote
3
replies
100
views
Extract specific portion of a string and paste to a new column in R
Rscript
tidyr
dataframe
tidyverse
offtopic
updated 3 days ago by
Marcel Ramos
570 • written 13 days ago by
Nikhil
• 0
0
votes
2
replies
82
views
MBD-seq non model species
MethylSeq
ramwas
MEDIPS
qsea
updated 3 days ago by
Simon Pearce
• 0 • written 14 days ago by
Marianna
• 0
0
votes
1
reply
53
views
DESeq errpr in normalizePath
DESeq2
updated 3 days ago by
Michael Love
37k • written 5 days ago by
ummscr
• 0
2
votes
2
replies
117
views
paired samples, comparing expression given a continuous variable
limma
updated 3 days ago by
Gordon Smyth
46k • written 4 days ago by
naz
• 0
0
votes
3
replies
124
views
I cannot install "microbiome"
GenomeInfoDbData
microbiome
phyloseq
updated 4 days ago by
Marcel Ramos
570 • written 7 days ago by
kikiki
• 0
4
votes
6
replies
6.4k
views
GSEA preranked analysis downstream of DEseq2
deseq2
gsea
rnaseq
updated 4 days ago by
hermidalc
▴ 10 • written 6.0 years ago by
EJ
▴ 10
0
votes
2
replies
75
views
DESeq2 LFC changes sign after adjusting for surrogates
sva
DESeq2
7 days ago • updated 4 days ago
Marie
• 0
3
votes
2
replies
69
views
how to use Rsamtools to parse extra fields from STAR alignment
Rsamtools
5 days ago • updated 4 days ago
Jiping Wang
▴ 90
25
votes
19
replies
19k
views
Mapping genome regions to gene symbols
tcga cnv
gene symbol
coordinate
updated 4 days ago by
michaelwegert
• 0 • written 7.3 years ago by
NS
▴ 60
0
votes
0
replies
20
views
DEXSeq aggregated genes/exons result in NA values
RNASeq
R
DEXSeq
4 days ago
osieman52
• 0
0
votes
1
reply
46
views
OPLS-DA: confidence interval for accuracy metric
Metabolomics
updated 4 days ago by
etienne.thevenot
▴ 20 • written 6 days ago by
Eddie
• 0
4
votes
10
replies
1.3k
views
Data input for aracne2regulon function in viper package
viper
updated 4 days ago by
xlal
• 0 • written 3.0 years ago by
maya.kappil
▴ 20
5
votes
1
reply
2.7k
views
Error with DropletUtils::EmptyDrops()
DropletUtils
EmptyDrops
simpleSingleCell
updated 4 days ago by
stefano.mangiola
• 0 • written 3.0 years ago by
shbrief
▴ 20
0
votes
0
replies
27
views
biomaRt, Ensembl, retrieve "Phenotypes" information
Ensembl
biomaRt
5 days ago
Hector
• 0
2
votes
3
replies
101
views
unable to install.packages("spatialLIBD")
spatialLIBD
updated 5 days ago by
Leonardo Collado Torres
▴ 1000 • written 5 days ago by
kstern
• 0
1
vote
2
replies
81
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
5 days ago
Delta._.43
▴ 20
0
votes
0
replies
27
views
A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation
wateRmelon
Computation
minfi
5 days ago
calen.p.ryan
• 0
1
vote
1
reply
70
views
spot- vs cell-level data access
spatialLIBD
updated 5 days ago by
Leonardo Collado Torres
▴ 1000 • written 6 days ago by
kstern
• 0
0
votes
2
replies
72
views
Question regarding averaging DESeq2 results.
DESeq2
6 days ago • updated 5 days ago
e.v.egeland
• 0
3
votes
2
replies
136
views
MEDIPS for chIP-Seq
ChIPSeq
10 days ago • updated 5 days ago
Darek
▴ 10
0
votes
0
replies
47
views
Normalization RNA-seq data maSigPro
maSigPro
5 days ago
W.a.m.dekker
• 0
4
votes
4
replies
174
views
Which is the best type of data for correlation or survival analysis
TPM
RNASeq
RSEM
DESeq2
9 days ago • updated 5 days ago
Yang Shi
• 0
0
votes
2
replies
78
views
MAI error - vector size limit
randomForest
MAI
updated 5 days ago by
jonathan.dekermanjian
• 0 • written 11 days ago by
Hans-Ulrich Klein
▴ 330
0
votes
7
replies
634
views
CHIPQC error regarding BiocParallel
CHIPQC
Diffbind
chipseq
rory stark
Thomas Carroll
updated 5 days ago by
arisarkar88
• 0 • written 2.3 years ago by
bioinfouser2
▴ 10
0
votes
0
replies
38
views
Statistical test for genomic annotation by ChIPseeker
statistics
PeakAnnotation
ChIPseeker
GuangchuangYu
5 days ago
arisarkar88
• 0
0
votes
7
replies
814
views
LFQ shiny app from DEP package reports: Error: 'imputeMethods' is not an exported object from 'namespace:MSnbase'
MSnbase
MsCoreUtils
DEP
updated 6 days ago by
Malcolm Cook
★ 1.6k • written 5 months ago by
Tobias
▴ 30
0
votes
2
replies
328
views
Error in trying to use Interactive analysis using the DEP Shiny apps (LFQ app)
LFQ
updated 6 days ago by
Malcolm Cook
★ 1.6k • written 6 months ago by
maria.kokolaki
• 0
1
vote
1
reply
76
views
ordinal treatment group design / contrast matrix
limma
updated 6 days ago by
James W. MacDonald
60k • written 7 days ago by
Chris
• 0
42,947 results • Page
1 of 859
Recent ...
Replies
Comment: errors in annotation
by
Josie
• 0
OK thanks James. I'll send off an email to GenBank, see if they feel inclined to correct some errors.
Answer: Conversion of UniProt to Ensembl
by
James W. MacDonald
60k
I will provide an example below. But first, there is a vignette for biomaRt (actually two), and it has extensive examples of how to use the…
Comment: the difference between getGEO and getGEOSuppFiles
by
Fatemeh
• 0
thank you!
Answer: the difference between getGEO and getGEOSuppFiles
by
James W. MacDonald
60k
When submitting data to GEO, you are supposed to provide both the raw data and a matrix of processed data. When you use `getGEO` you get th…
Comment: error running UniProt.ws
by
James W. MacDonald
60k
https://www.bioconductor.org/checkResults/3.15/bioc-LATEST/UniProt.ws/nebbiolo1-install.html
Votes
Answer: Error in Create switchAnalyzeRlist
Answer: Error in Create switchAnalyzeRlist
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
Answer: the difference between getGEO and getGEOSuppFiles
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Gordon Smyth
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