0
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0
replies
884
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clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
2.2 years ago nromerov • 0
1
vote
3
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910
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edgeR: Time course RNA-seq experiments
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3
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5
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DESeq2: Design model includes sex but only one female
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updated 2.2 years ago by 43k • written 2.2 years ago by • 0
0
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3
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Installing Gpart
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updated 2.2 years ago by 68k • written 2.2 years ago by • 0
2
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1
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1.5k
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limma::topTable with adjust.method=NULL is not BH corrected (manual is inconsistent with behavior?)
Bioconductor biocon limma
updated 2.2 years ago by 53k • written 2.2 years ago by • 0
1
vote
7
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1.8k
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DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 2.0 years ago by 53k • written 2.2 years ago by • 0
2
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2
replies
887
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SeqSQC R library, functions PCA and IBD not working
SeqSQC
2.2 years ago ttom ▴ 10
0
votes
1
reply
1.7k
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DeSeq2 normalization 16S
DESeq2
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
5
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3
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limma: More differentially expressed genes when factor included in model than when used as blocking factor
voom blocking limma
updated 2.2 years ago by 53k • written 2.2 years ago by ▴ 180
0
votes
4
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1.5k
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DESeq2 : standardising variation between treatments
RNA-seq DESeq2
2.2 years ago ar14g12 • 0
0
votes
2
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872
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Issues with ddseq2 for treatment response factoring in different KO clones
Clonality RNASeq DESeq2
updated 2.2 years ago by ★ 1.4k • written 2.2 years ago by • 0
0
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1
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1.1k
views
Subsetting cells from a single cell experiment
SingleCellExperiment
written 2.2 years ago by • 0
0
votes
0
replies
582
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loadstudy and cBioDataPack return error in vroom_
cBioPortalData
2.2 years ago karam • 0
0
votes
1
reply
925
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DeSeq2 data comparison and extracting outputs
DESeq2
updated 2.2 years ago by ★ 1.4k • written 2.2 years ago by • 0
0
votes
1
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1.4k
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EPIC v2 demo data from blood samples
MethylationArray methylationArrayAnalysis
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
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0
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974
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DiffBind dba.count() crash/can't finish problems
dba.count DiffBind ATACSeq
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
2
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4
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1.9k
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DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 2.2 years ago by ▴ 10 • written 2.2 years ago by • 0
2
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2
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920
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DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
2.2 years ago r.murakami • 0
0
votes
3
replies
1.4k
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minfi bumphunter - probe IDs
minfi bumphunter
updated 2.2 years ago by ▴ 780 • written 2.2 years ago by • 0
0
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2
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1.4k
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scRNA analysis : DEG between low and high-expressing cells
scRNAseq
2.2 years ago Momo • 0
0
votes
5
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1.5k
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pathway finding software
written 17.1 years ago by ▴ 250
0
votes
1
reply
738
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how to extract specific gene coordinates by passing a list of genes using homo.sapiens library
missRows
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
10
votes
11
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3.6k
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tximport error: vroom
tximport
updated 2.1 years ago by • 0 • written 2.2 years ago by ▴ 40
0
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1
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833
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Gene names from Matrix
BioCor StarBioTrek MatrixGenerics
updated 20 months ago by ▴ 760 • written 2.2 years ago by • 0
2
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11
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Error MakeOrgPackagefromNCBI
Bioconductor
updated 22 months ago by ★ 4.1k • written 2.2 years ago by • 0
0
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5
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3.0k
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Gviz: UcscTrack and "GC Percent" information
Gviz coMET
3.0 years ago • updated 2.2 years ago Daniel E. Weeks ▴ 30
1
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4
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6.1k
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How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray Preprocessing NimbleGen Normalization
written 3.1 years ago by • 0
1
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5
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Mixed up sample info with plotPCA
plotMA ggplot2 plotPCA DESeq2
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
2
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6
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1.6k
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Biostrings error at retrieving protein sequences
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updated 2.2 years ago by 16k • written 2.2 years ago by • 0
0
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4
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Extract LRT results for each comparison
LRT DESeq2
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
0
votes
2
replies
970
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bug in block.plsda from mixOmics?
mixOmics
2.2 years ago Lluís Revilla Sancho ▴ 760
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1
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748
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Is SeqSQC compatible with hg38?
SeqSQC hg38
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
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2
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using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
2.2 years ago Gregory • 0
0
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1
reply
1.1k
views
Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 2.2 years ago by ▴ 780 • written 2.2 years ago by • 0
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1
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1.2k
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DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
1
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4
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1.5k
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biomaRt code/getBM function no longer importing 'coding' sequence via seqType argument, "Invalid attribute(s): coding" error
biomaRt
2.2 years ago andrew.b.kleist ▴ 10
5
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2
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2.8k
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ComBat_seq function in sva package does not return a matrix
sva ComBat ComBat-seq Bioconductor ComBat_seq
2.2 years ago Federico ▴ 10
0
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1
reply
709
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error running exp2grn
NewWave
updated 2.2 years ago by ▴ 40 • written 2.3 years ago by • 0
0
votes
2
replies
880
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Singlecell protein surface (ADT) pseudotime techniques
monocle slingshot
2.2 years ago EspressoKris ▴ 10
0
votes
3
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829
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shinyMethyl - saving the file
shinyMethyl
2.2 years ago dorota.komar • 0
2
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4
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Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
2.2 years ago Shihui • 0
0
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3
replies
1.2k
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Suggested package missing from Development version of Bioconductor
Devel
updated 2.2 years ago by 4.2k • written 2.2 years ago by • 0
0
votes
0
replies
672
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mixOmics with Bioconductor classes
mixOmics
2.2 years ago Lluís Revilla Sancho ▴ 760
0
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0
replies
875
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featureCounts error Assertion failed: (NULL == pairer -> bam_margin_table -> appendix2), function SAM_pairer_finish_margin_table, file input-files.c,…
NewWave
2.2 years ago Kilian • 0
0
votes
1
reply
865
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Batch effect adjust in model matrix
BatchEffect edgeR
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
0
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1
reply
706
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HTSeqGenie runs very slow
HTSeqGenie
2.2 years ago zh9118 • 0
0
votes
0
replies
818
views
Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
2.2 years ago franciscrick41 • 0
5
votes
9
replies
2.8k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 20 months ago by 53k • written 2.2 years ago by ▴ 10
0
votes
5
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1.2k
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DESeq2, results(dds, name = <reference>) interpretation results
DESeq2
2.2 years ago Rockbar • 0
0
votes
2
replies
2.3k
views
For R version 4.0.2 and Biconductor version 3.11, clusterProfiler is not working
Bioconductor clusterProfiler
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
46,693 results • Page 41 of 934
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Normalizing complex datasets like Hi C can be challenging, much like setting up a PC for optimal gaming performance. Just as careful tuning…
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Thanks for sharing your question about RMA limma analysis While working on your experiment, it s always helpful to have some background mu…
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You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
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