0
votes
1
reply
571
views
Samples have been merged or lost during counting. Check for duplicate bam files. DiffBind dbacount
DiffBind
8 months ago Mark • 0
0
votes
1
reply
560
views
CopywriteR output
CopywriteR
updated 6 weeks ago by • 0 • written 2.5 years ago by • 0
0
votes
3
replies
560
views
Suggested package missing from Development version of Bioconductor
Devel
updated 7 months ago by 3.9k • written 7 months ago by • 0
0
votes
0
replies
559
views
SSL connect error in e.g. pathview from R version 4 in Windows 10
pathview SSL curl
10 months ago Matthias • 0
2
votes
4
replies
552
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 4 months ago by 50k • written 5 months ago by • 0
0
votes
0
replies
551
views
what should be the input for SingleR() automatic cell type annotation?
SingleR
11 months ago Yijing • 0
0
votes
2
replies
545
views
No compilation on Windows y compilation on linux
Devel PackageType deve
12 months ago • updated 11 months ago Franck RICHARD • 0
0
votes
1
reply
539
views
GenomicDataCommons: Retrieve patient data for RPPA samples
TCGA GenomicDataCommons GDC
written 10 months ago by ▴ 510
0
votes
1
reply
535
views
Gene enrichment analysis
analysis R GOfuncR
updated 11 months ago by ▴ 730 • written 11 months ago by • 0
2
votes
1
reply
528
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA wgcna_package
updated 11 months ago by ▴ 50 • written 12 months ago by ▴ 10
0
votes
1
reply
524
views
Cibersort phenotype file
cibersort deconvR immune
updated 5 weeks ago by • 0 • written 15 months ago by • 0
0
votes
1
reply
523
views
Subsetting cells from a single cell experiment
SingleCellExperiment
written 7 months ago by • 0
0
votes
2
replies
512
views
Recount3: PCR duplicates
pcrduplicates recount3 multimappingreads
updated 11 months ago by • 0 • written 11 months ago by • 0
1
vote
4
replies
511
views
EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation MethylationArray methylationArrayAnalysis illumina
3 months ago mikat • 0
0
votes
0
replies
509
views
Model matrix for a complex study design using aldex.glm module from ALDEx2 R package
ALDEx2 modelmatrix covariates
10 months ago amir • 0
0
votes
2
replies
497
views
can't update bioconductor 3.18
BioCor bioc BiocVersion
6 months ago feifan • 0
0
votes
3
replies
496
views
determine if R package or it's dependencies functionality require internet access
biomaRt
updated 6 months ago by 50k • written 6 months ago by • 0
1
vote
5
replies
493
views
BiomaRt download data error
biomaRt
updated 3 months ago by ★ 6.5k • written 3 months ago by • 0
1
vote
0
replies
493
views
WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 11 months ago by 42k • written 12 months ago by ▴ 20
2
votes
13
replies
492
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
28 days ago • updated 25 days ago fernanda.backsouza ▴ 10
0
votes
2
replies
490
views
Can you help me generate a Bsgenome of the fusion genome of a human and HIV-1 virus?
BSgenome.Hsapiens.NCBI.GRCh38
6 months ago 13273976287 • 0
0
votes
0
replies
487
views
Variant Filtering on very large VCF files
VariantAnnotation VariantFiltering
7 months ago Bogdan ▴ 670
0
votes
0
replies
485
views
Can't get working R 3.6.3 and 4.2.3 with DESEq2 if compiled by AMD CLANG at Ubuntu 22.04 x64
CLANG DESeq2
10 months ago lokapal • 0
0
votes
0
replies
480
views
Version map cannot be validated - not mapping to new bioconductor website
Install
6 months ago Alexander • 0
1
vote
1
reply
479
views
Rbowtie2 problem
Rbowtie2
updated 4 months ago by • 0 • written 23 months ago by ▴ 10
0
votes
1
reply
476
views
Running DNAbarcodes with 12bp
dnabarcodes
updated 3 months ago by • 0 • written 3.9 years ago by • 0
0
votes
0
replies
470
views
MethylKit::calculateDiffMeth with two experimental factors
methylKit
9 months ago Andrés • 0
2
votes
6
replies
469
views
How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
5 weeks ago Chris ▴ 10
0
votes
1
reply
467
views
customProDB easyrun error in generating a custom protein database: Error in keepSeqlevels(anno, seqlevels(galn), pruning.mode = "coarse")
customProDB
11 months ago Esraa • 0
1
vote
0
replies
465
views
Gviz : UcscTrack
rtracklayer UCSC Gviz
6 months ago yujin ▴ 10
0
votes
1
reply
465
views
HiCDCPlus `construct_features` incompatible with BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0 annotation
HiC-DC+ HiCDCPlus
updated 11 months ago by • 0 • written 17 months ago by • 0
1
vote
0
replies
463
views
Differential abundance analysis of phosphoproteomics data with multiple time points and conditions
Proteomics DifferentialRegulation limma
8 months ago svlachavas ▴ 830
0
votes
3
replies
462
views
Unable to install clusterProfiler
clusterProfiler
updated 3 months ago by • 0 • written 3 months ago by • 0
0
votes
2
replies
461
views
DESeq2: how could the lower mean abundance treatment show a positive and significant LFC?
DESeq2
7 months ago • updated 6 months ago Roey Angel • 0
0
votes
0
replies
461
views
Issues setting background in STRINGdb
STRINGdb MSstats
11 months ago samsiljee • 0
3
votes
3
replies
459
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater runPCA
updated 8 weeks ago by ▴ 160 • written 8 weeks ago by • 0
0
votes
1
reply
456
views
HiCDCPlus glm.fit error
HiCDCPlus
updated 11 months ago by • 0 • written 12 months ago by • 0
0
votes
1
reply
453
views
Error with IsoformSwitchAnalyzer: analyzePFAM
IsoformSwitchAnalyzeR
11 months ago Callum • 0
0
votes
0
replies
450
views
Positive beta-scores of essential genes in drug-treated cells
mageck MAGeCKFlute CrisprScreen
11 months ago Monika • 0
0
votes
0
replies
450
views
DEG after deconvolution of GeoMx Spatial data using scRNA-seq reference
GeoMx DifferentialExpression GeomxTools
updated 10 months ago by 65k • written 10 months ago by • 0
1
vote
0
replies
449
views
subsetByOverlaps in GenomicInteractions object doesn't work properly?
InteractionSet subsetByOverlaps GenomicInteractions
10 months ago LaureTomas ▴ 10
0
votes
2
replies
447
views
Cannot open Sysmex Partec CUbe 6 .fcs with read.FCS
Partec read.FCS flowCore
6 months ago mrescan • 0
0
votes
0
replies
446
views
Help with error running DiffBind
DiffBind
11 months ago Chris ▴ 10
0
votes
7
replies
444
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages Proxy Bioconductor GEOquery Internet_connection_problem
7 weeks ago • updated 6 weeks ago needNGS • 0
0
votes
0
replies
441
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
12 months ago Levi • 0
3
votes
1
reply
441
views
NPARC package y-variable
NPARC NPA
updated 8 months ago by ▴ 20 • written 8 months ago by • 0
0
votes
1
reply
433
views
Problems when running GDC_prepare in R
TCGAbiolinks error GDC_prepare
6 months ago leon • 0
0
votes
0
replies
430
views
DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 7 months ago by 65k • written 7 months ago by • 0
0
votes
0
replies
427
views
mzTab-M in XCMS
xcms mzTab-M iterativehierarchicalprocessing FBMN
11 months ago Abrianna • 0
1
vote
1
reply
426
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
updated 6 months ago by ▴ 190 • written 6 months ago by ▴ 10
403 results • Page 3 of 9
Recent ...
Replies
Answer: ERROR; return code from pthread_create() is 22 by James W. MacDonald 65k
Seems OK to me. ``` > dat <- ReadAffy() > dat AffyBatch object size of arrays=744x744 features (20 kb) cdf=HG-U219 (49386 affyids) …
Answer: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 65k
Unless you think the different lines or tissues will have very different within-group variances, you should just analyze together and make …
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments? by James W. MacDonald 65k
It appears that batch is orthogonal to the treatment, so you can just fit a batch effect in your model.
Answer: Control group between 2 batches have different expression in RNAseq data by James W. MacDonald 65k
Since batch is orthogonal to the treatment, you just add a batch factor to your model.
Answer: Subsetting RNAseq data | voomaByGroup() by Anna • 0
Hi Gordon. Thank you so much. Your reply is extremely helpful, and I feel more confident moving forward with the analysis. Also, very inte…
Votes
Answer: Subsetting RNAseq data | voomaByGroup()
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Awards • All
Popular Question to shepherl 3.9k
Popular Question to Hussain • 0
Popular Question to euge.eugenio ▴ 20
Popular Question to Dario Strbenac ★ 1.5k
Popular Question to Vincent J. Carey, Jr. 6.7k
Locations • All
Italy, just now
United States, 6 minutes ago
Sweden, 7 minutes ago
United States, 8 minutes ago
Sweden, 12 minutes ago
Traffic: 720 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6