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
5 weeks ago Maliha Tabassum • 0
0
votes
1
reply
145
views
what is the sampleFiles
chipseq
updated 6 weeks ago by 66k • written 6 weeks ago by • 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 ★ 4.2k • written 6 weeks ago by • 0
2
votes
2
replies
201
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 ▴ 850 • written 6 weeks ago by • 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
164
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
222
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 6 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
0
votes
0
replies
136
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 66k • written 8 weeks ago by • 0
0
votes
2
replies
320
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
460
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 66k • written 8 weeks ago by • 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 ▴ 160 • written 9 weeks ago by • 0
0
votes
0
replies
154
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals GenomicRanges
9 weeks ago gshweta95 • 0
2
votes
1
reply
252
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 9 weeks ago by ★ 4.0k • written 9 weeks ago by ▴ 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 700 • written 9 weeks ago by • 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 9 weeks ago by • 0
1
vote
2
replies
332
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 9 weeks ago by ★ 4.2k • written 9 weeks ago by • 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 ▴ 20 • written 10 weeks ago by • 0
0
votes
2
replies
322
views
Error in msaFun Cannot open input file. No alignment!
msa
written 10 weeks ago by ▴ 30
0
votes
1
reply
214
views
Help with identifying genes mapped to KEGG pathway using pathview
pathview
updated 8 weeks ago by ★ 4.0k • written 10 weeks ago by • 0
0
votes
1
reply
205
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 10 weeks ago by 50k • written 10 weeks ago by ▴ 180
0
votes
2
replies
284
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 • 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
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11 weeks ago bocsci11 • 0
1,000 results • Page 2 of 20
Recent ...
Replies
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 …
Answer: Counter-directional LFC shrinkage by Michael Love 42k
It's not just the average count but also the dispersion that affects apeglm. You can try ashr for another type of shrinkage.
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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