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0
votes
4
replies
283
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
5 weeks ago
lonn
• 0
0
votes
0
replies
99
views
Enzyme Engineering
BioTIP
5 weeks ago
bocchemistry
• 0
0
votes
0
replies
114
views
Syntaxt Error in IsorcorrectoR package with Molecule Info File
Syntaxerror
IsoCorrectoR
6 weeks ago
Maliha Tabassum
• 0
0
votes
1
reply
145
views
what is the sampleFiles
chipseq
updated 6 weeks ago by
James W. MacDonald
66k • written 6 weeks ago by
zhulin
• 0
0
votes
0
replies
114
views
Diffbind Error in socketConnection
DiffBind
Errorinsocketconnection
SpikeIn
6 weeks ago
Virangika
• 0
0
votes
0
replies
92
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
6 weeks ago
Henry
▴ 10
0
votes
1
reply
158
views
Deseq2 Rlog transformation
DESeq2
updated 6 weeks ago by
ATpoint
★ 4.2k • written 6 weeks ago by
Sahar
• 0
2
votes
2
replies
202
views
[DiffBind] Obtaining normalization factors
DiffBind
6 weeks ago
Henry
▴ 10
0
votes
3
replies
298
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq
sva
updated 5 weeks ago by
W. Evan Johnson
▴ 850 • written 6 weeks ago by
schlumbohm
• 0
0
votes
0
replies
109
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
6 weeks ago
Stevie Pederson
• 0
3
votes
6
replies
326
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
6 weeks ago
nhaus
▴ 40
0
votes
1
reply
206
views
DESeq2 gives an error and R crashes
DESeq2
6 weeks ago
Shefali
• 0
0
votes
0
replies
165
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
6 weeks ago
Eryn
• 0
0
votes
0
replies
102
views
queryDGIdb lexical error for some genes
lexicalerror
rDGIdb
DGIdb
json
6 weeks ago
Dennis
• 0
0
votes
1
reply
224
views
compareCluster dotplot: how to modify the genesets order
DOSE
enrichplot
clusterProfiler
updated 6 weeks ago by
Guido Hooiveld
★ 4.0k • written 6 weeks ago by
Lucie
• 0
0
votes
0
replies
137
views
ggtree tip label position (depth)
ggtree
7 weeks ago • updated 6 weeks ago
Roope
• 0
2
votes
6
replies
513
views
How to make boxplot with pairwise and overall p value from Limma
t.test
boxplot
limma
anova
7 weeks ago
Chris
▴ 10
0
votes
0
replies
169
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler
gseKEGG
7 weeks ago
andromeda
• 0
0
votes
1
reply
149
views
Granges regionCounts not returning the expected number of entries
methylKit
7 weeks ago
Modoc Kesner
▴ 10
0
votes
0
replies
121
views
flowDensity on a flowset
flowDensity
7 weeks ago
fredrikwallberg
• 0
0
votes
0
replies
108
views
DMRcate error need at least two non-NA values to interpolate
DNAMethylation
DMRcate
7 weeks ago
Macsue
• 0
0
votes
1
reply
178
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 8 weeks ago by
James W. MacDonald
66k • written 8 weeks ago by
ja569116
• 0
0
votes
2
replies
321
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
8 weeks ago • updated 7 weeks ago
fer_talavera
• 0
0
votes
2
replies
292
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
8 weeks ago • updated 5 weeks ago
isaac.vock
• 0
0
votes
7
replies
461
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
8 weeks ago
needNGS
• 0
0
votes
0
replies
129
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
8 weeks ago
feather-W
• 0
0
votes
0
replies
132
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
8 weeks ago
Ankit
▴ 20
1
vote
5
replies
381
views
fgsea fork
fgsea
updated 8 weeks ago by
James W. MacDonald
66k • written 8 weeks ago by
yimjohns
• 0
0
votes
0
replies
118
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
8 weeks ago
Pierre Lindenbaum
▴ 10
3
votes
3
replies
477
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 9 weeks ago by
alan.ocallaghan
▴ 160 • written 9 weeks ago by
Najla Abassi
• 0
0
votes
0
replies
155
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
9 weeks ago
gshweta95
• 0
2
votes
1
reply
253
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 9 weeks ago by
Guido Hooiveld
★ 4.0k • written 9 weeks ago by
enee
▴ 10
0
votes
0
replies
128
views
Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
9 weeks ago
nromerov
• 0
1
vote
3
replies
284
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 9 weeks ago by
Marcel Ramos
700 • written 9 weeks ago by
Astrid Deschênes
• 0
0
votes
0
replies
149
views
crlmm: CDF for Infinium Global Diversity Array By Illumina
globaldiversityarray
cdf
crlmm
9 weeks ago
mayra.haedo
• 0
0
votes
0
replies
159
views
Multifactor analysis in DiffBind
DiffBind
multifactoranalysis
9 weeks ago
erbrocato
• 0
1
vote
4
replies
331
views
EDAseq to normalise for both gene-length and GC-content
norma
EDASeq
EDA
Normalization
9 weeks ago
samuel.channon
• 0
0
votes
2
replies
239
views
Visium RNA
metaMSdata
written 10 weeks ago by
Karlison
• 0
1
vote
2
replies
334
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 9 weeks ago by
ATpoint
★ 4.2k • written 10 weeks ago by
maximilian.beikirch
• 0
0
votes
0
replies
127
views
DNAcopy segment function not reproducible even when setting seed
DNAcopy
10 weeks ago
BID
• 0
2
votes
3
replies
307
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 8 weeks ago by
mercedeh.movassagh
▴ 20 • written 10 weeks ago by
María
• 0
0
votes
2
replies
324
views
Error in msaFun Cannot open input file. No alignment!
msa
written 10 weeks ago by
Kamil Slowikowski
▴ 30
0
votes
1
reply
215
views
Help with identifying genes mapped to KEGG pathway using pathview
pathview
updated 9 weeks ago by
Guido Hooiveld
★ 4.0k • written 10 weeks ago by
Julie
• 0
0
votes
1
reply
207
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 10 weeks ago by
Gordon Smyth
50k • written 10 weeks ago by
Gerhard Thallinger
▴ 180
0
votes
2
replies
285
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
11 weeks ago • updated 10 weeks ago
Sam
▴ 10
0
votes
1
reply
267
views
TCGA clinical data: Multiple measure of response columns in merged clinical xml file.
TCGAbiolinks
TCGA
clinical
TCGA-BRCA
written 11 weeks ago by
BioinfoMug
• 0
0
votes
1
reply
225
views
Exact same results in Diffbind with different normalization methods
DiffBind
11 weeks ago • updated 10 weeks ago
red_bricks
▴ 50
0
votes
0
replies
149
views
FELLA plotGraph function won't change the legend
FELLA
11 weeks ago
yuhang
• 0
0
votes
0
replies
185
views
medips-output
ngsReports
MEDIPS
11 weeks ago
Researcher
• 0
0
votes
0
replies
161
views
Join BOC Sciences at Drug Discovery Chemistry
alabaster.schemas
db0
11 weeks ago
bocsci11
• 0
1,000 results • Page
2 of 20
Recent ...
Replies
Comment: Cannot install oligo on Fedora
by
Guido Hooiveld
★ 4.0k
Thanks for all suggestions and getting to the bottom of this! Unfortunately, fixing C code goes way above my skill level, so I cannot contr…
Comment: Cannot install oligo on Fedora
by
James W. MacDonald
66k
I think the solution is for the C code in `oligo` to be updated to work with more modern versions of `zlib`. The `zlibbioc` package is real…
Comment: Error in gseDO function
by
Guido Hooiveld
★ 4.0k
I don't fully understand what you are asking... Yet, in my opinion it doesn't make sense to use the results of only 12 genes for ORA (nor G…
Comment: Counter-directional LFC shrinkage
by
ATpoint
★ 4.2k
Is this RNA-seq? The unshrunken MA-plot looks very odd and indicates that normalization is completely offset.
Answer: ChAMP not available for bioconductor 3.19
by
shepherl
3.9k
See https://support.bioconductor.org/p/9158324/#9158336 . We have reached out to goseq to fix the package; we have a community member …
Votes
A: DESeq2: add annotations (from data frame) to DESeqDataSet
Answer: Error in gseDO function
Comment: what the test method for enrichGO in clusterProfiler?
A: Comparison between two different group's pathway analysis results
DiffBind Batch Effect
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