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0
votes
0
replies
112
views
flowDensity on a flowset
flowDensity
5 weeks ago
fredrikwallberg
• 0
0
votes
0
replies
102
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
5 weeks ago
Macsue
• 0
0
votes
1
reply
172
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
ja569116
• 0
0
votes
2
replies
310
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
6 weeks ago • updated 5 weeks ago
fer_talavera
• 0
0
votes
2
replies
269
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
6 weeks ago • updated 26 days ago
isaac.vock
• 0
0
votes
7
replies
428
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
6 weeks ago
needNGS
• 0
0
votes
0
replies
121
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
6 weeks ago
feather-W
• 0
0
votes
0
replies
118
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
6 weeks ago
Ankit
▴ 20
1
vote
5
replies
357
views
fgsea fork
fgsea
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
yimjohns
• 0
0
votes
0
replies
107
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
6 weeks ago
Pierre Lindenbaum
▴ 10
3
votes
3
replies
441
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 7 weeks ago by
alan.ocallaghan
▴ 160 • written 7 weeks ago by
Najla Abassi
• 0
0
votes
0
replies
137
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
7 weeks ago
gshweta95
• 0
2
votes
1
reply
224
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 7 weeks ago by
Guido Hooiveld
★ 4.0k • written 7 weeks ago by
enee
▴ 10
0
votes
0
replies
122
views
Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
7 weeks ago
nromerov
• 0
1
vote
3
replies
267
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 7 weeks ago by
Marcel Ramos
690 • written 7 weeks ago by
Astrid Deschênes
• 0
0
votes
0
replies
138
views
crlmm: CDF for Infinium Global Diversity Array By Illumina
globaldiversityarray
cdf
crlmm
8 weeks ago
mayra.haedo
• 0
0
votes
0
replies
123
views
Macsquant FCS in read.FCS & opencyto
FlowCytometry
flowWorkspace
flowCore
8 weeks ago
taylor.witte
• 0
0
votes
0
replies
147
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
8 weeks ago
erbrocato
• 0
1
vote
4
replies
309
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
8 weeks ago • updated 7 weeks ago
samuel.channon
• 0
0
votes
2
replies
212
views
Visium RNA
metaMSdata
updated 8 weeks ago by
vvvc360work2
• 0 • written 8 weeks ago by
Karlison
• 0
1
vote
2
replies
303
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 8 weeks ago by
ATpoint
★ 4.1k • written 8 weeks ago by
maximilian.beikirch
• 0
0
votes
0
replies
118
views
DNAcopy segment function not reproducible even when setting seed
DNAcopy
8 weeks ago
BID
• 0
1
vote
3
replies
287
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 6 weeks ago by
mercedeh.movassagh
▴ 10 • written 8 weeks ago by
María
• 0
0
votes
2
replies
278
views
Error in msaFun Cannot open input file. No alignment!
msa
written 8 weeks ago by
Kamil Slowikowski
▴ 30
0
votes
1
reply
202
views
Help with identifying genes mapped to KEGG pathway using pathview
pathview
updated 7 weeks ago by
Guido Hooiveld
★ 4.0k • written 8 weeks ago by
Julie
• 0
0
votes
1
reply
191
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 8 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
Gerhard Thallinger
▴ 180
0
votes
2
replies
266
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
9 weeks ago • updated 8 weeks ago
Sam
▴ 10
0
votes
1
reply
246
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks
TCGA
clinical
TCGA-BRCA
written 9 weeks ago by
BioinfoMug
• 0
0
votes
1
reply
208
views
Exact same results in Diffbind with different normalization methods
DiffBind
9 weeks ago • updated 8 weeks ago
red_bricks
▴ 50
0
votes
0
replies
136
views
FELLA plotGraph function won't change the legend
FELLA
9 weeks ago
yuhang
• 0
0
votes
0
replies
163
views
medips-output
ngsReports
MEDIPS
9 weeks ago
Researcher
• 0
0
votes
0
replies
152
views
Join BOC Sciences at Drug Discovery Chemistry
alabaster.schemas
db0
9 weeks ago
bocsci11
• 0
0
votes
0
replies
119
views
The graphical interface of FELLA doesn't work
FELLA
9 weeks ago
yuhang
• 0
0
votes
0
replies
141
views
DEXSeq plot error
DEXSeq
DEXSeqNAvalues
DEXseq
9 weeks ago
jean-christophe.helbling
• 0
0
votes
0
replies
166
views
To analyze StringTie data using the isoformSwitchAnalyzeR package
IsoformSwitchAnalyzeR
9 weeks ago
Henry
• 0
0
votes
1
reply
250
views
Rcpp compilation error
Release
Rcpp
updated 9 weeks ago by
ATpoint
★ 4.1k • written 9 weeks ago by
Robert K. Bradley
▴ 40
0
votes
0
replies
190
views
Rain error: invalid annotation of time points
rain
9 weeks ago
mpuli011
• 0
0
votes
0
replies
213
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi
minfiDataEPIC
9 weeks ago
Felix
• 0
0
votes
0
replies
164
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
10 weeks ago • updated 8 weeks ago
Giovanni Calice
▴ 160
0
votes
0
replies
235
views
Error: grouping factors must have > 1 sampled level
Mast
mastR
MAST
updated 10 weeks ago by
James W. MacDonald
65k • written 10 weeks ago by
Andrew
• 0
0
votes
0
replies
155
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts
Rsubread
10 weeks ago
chris2.a.white
• 0
0
votes
0
replies
177
views
Could SGSeq utilizes "ts" tag produced from minimap2 other than "XS" tag?
XS-tag
SplicedAlignment
SGSeq
minimap2
10 weeks ago
jk
• 0
0
votes
0
replies
162
views
Can I combine collinear variables into a single value
BatchEffect
limma
10 weeks ago
Harrsha
• 0
0
votes
0
replies
252
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
10 weeks ago
vipul14
• 0
0
votes
0
replies
124
views
Issue with shiftGAlignmentsList() in ATACseqQC after updating
R
ATACseqQC
10 weeks ago
danalvoronov
▴ 10
0
votes
0
replies
152
views
lfcSE
RGSEA
11 weeks ago
Gordon
• 0
0
votes
4
replies
319
views
Interactions in batches of varying size with different number of replicates using limma
limma
RNASeq
DifferentialExpression
11 weeks ago • updated 10 weeks ago
mperalc
• 0
1
vote
0
replies
184
views
Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k
MethylationArray
TCGAbiolinks
Tcga
TCGAbiolinksGUI.data
11 weeks ago
BioinfoMug
• 0
0
votes
0
replies
167
views
Unclear exon-exon connection after RSubjunc() usage
IGV
Rsubjunc
Rsubread
11 weeks ago
thomas.heigl.ibk
• 0
0
votes
1
reply
260
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 11 weeks ago by
ATpoint
★ 4.1k • written 11 weeks ago by
sodiogoes
• 0
1,000 results • Page
2 of 20
Recent ...
Replies
Comment: error running enricher from clusterprofiler
by
Yael
• 0
It worked!!! Thanks alot, i think something in the gene_list wasnt right... Thanks agian
Comment: Create protein sequences including variants from a VCF file
by
Yun
• 0
This cannot work for a SNV file, since `injectSNPs` need a `SNPlocs` object
Comment: Can log2cpm be used for proteomics data normalization?
by
Daniel
• 0
Thank you for the quick reply and I apologize for it being on the wrong thread but the "post tag" function wasn't working properly.
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Patadù
▴ 10
I have arranged the code again following the other post and also the script you suggested. Now, I managed to install `org.Vdahliae.eg.db`. …
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Patadù
▴ 10
Thanks again Guido, I will try to run the script you have suggested and see if I can install the package. Yes, I have seen this message a…
Votes
Answer: Trim/Filter out-of-bounds GRanges
Comment: How to correctly adjust for gender in edgeR
Create protein sequences including variants from a VCF file
A: DEXSeq design formula
Answer: SGSeq: moving toward diffex from SGSeq analysis
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