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Votes
0
votes
0
replies
884
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler
DifferentialExpression
2.2 years ago
nromerov
• 0
1
vote
3
replies
910
views
edgeR: Time course RNA-seq experiments
edgeR
updated 2.2 years ago by
ATpoint
★ 5.0k • written 2.2 years ago by
SuperDad
• 0
3
votes
5
replies
1.7k
views
DESeq2: Design model includes sex but only one female
DESeq2
updated 2.2 years ago by
Michael Love
43k • written 2.2 years ago by
mphogan
• 0
0
votes
3
replies
1.5k
views
Installing Gpart
gpart
heat
heatmaps
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
Benjamin
• 0
2
votes
1
reply
1.5k
views
limma::topTable with adjust.method=NULL is not BH corrected (manual is inconsistent with behavior?)
Bioconductor
biocon
limma
updated 2.2 years ago by
Gordon Smyth
53k • written 2.2 years ago by
ningyuan
• 0
1
vote
7
replies
1.8k
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition
RNASeqData
limma
BulkRNAseq
RNASeq
updated 2.0 years ago by
Gordon Smyth
53k • written 2.2 years ago by
Gimena
• 0
2
votes
2
replies
887
views
SeqSQC R library, functions PCA and IBD not working
SeqSQC
2.2 years ago
ttom
▴ 10
0
votes
1
reply
1.7k
views
DeSeq2 normalization 16S
DESeq2
updated 2.2 years ago by
Michael Love
43k • written 2.2 years ago by
Alexis
• 0
5
votes
3
replies
1.3k
views
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
Gordon Smyth
53k • written 2.2 years ago by
Gerhard Thallinger
▴ 180
0
votes
4
replies
1.5k
views
DESeq2 : standardising variation between treatments
RNA-seq
DESeq2
2.2 years ago
ar14g12
• 0
0
votes
2
replies
872
views
Issues with ddseq2 for treatment response factoring in different KO clones
Clonality
RNASeq
DESeq2
updated 2.2 years ago by
swbarnes2
★ 1.4k • written 2.2 years ago by
Jules
• 0
0
votes
1
reply
1.1k
views
Subsetting cells from a single cell experiment
SingleCellExperiment
written 2.2 years ago by
megan
• 0
0
votes
0
replies
582
views
loadstudy and cBioDataPack return error in vroom_
cBioPortalData
2.2 years ago
karam
• 0
0
votes
1
reply
925
views
DeSeq2 data comparison and extracting outputs
DESeq2
updated 2.2 years ago by
swbarnes2
★ 1.4k • written 2.2 years ago by
sedabarutcu.a
• 0
0
votes
1
reply
1.4k
views
EPIC v2 demo data from blood samples
MethylationArray
methylationArrayAnalysis
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
henry-keen
• 0
0
votes
0
replies
974
views
DiffBind dba.count() crash/can't finish problems
dba.count
DiffBind
ATACSeq
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
sophie.hfliu
• 0
2
votes
4
replies
1.9k
views
DiffBind returns different grey lists every time I run dba.blacklist even if I set seed.
DiffBind
updated 2.2 years ago by
Matt Eldridge
▴ 10 • written 2.2 years ago by
r.murakami
• 0
2
votes
2
replies
920
views
DiffBind dba.analyze function doesn't have bSubControl option anymore?
DiffBind
2.2 years ago
r.murakami
• 0
0
votes
3
replies
1.4k
views
minfi bumphunter - probe IDs
minfi
bumphunter
updated 2.2 years ago by
Basti
▴ 780 • written 2.2 years ago by
dorota.komar
• 0
0
votes
2
replies
1.4k
views
scRNA analysis : DEG between low and high-expressing cells
scRNAseq
2.2 years ago
Momo
• 0
0
votes
5
replies
1.5k
views
pathway finding software
written 17.1 years ago by
Yanqin Yang
▴ 250
0
votes
1
reply
738
views
how to extract specific gene coordinates by passing a list of genes using homo.sapiens library
missRows
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
Tharun
• 0
10
votes
11
replies
3.6k
views
tximport error: vroom
tximport
updated 2.1 years ago by
Abhishek
• 0 • written 2.2 years ago by
RLiu
▴ 40
0
votes
1
reply
833
views
Gene names from Matrix
BioCor
StarBioTrek
MatrixGenerics
updated 20 months ago by
Lluís Revilla Sancho
▴ 760 • written 2.2 years ago by
karmasstark
• 0
2
votes
11
replies
2.0k
views
Error MakeOrgPackagefromNCBI
Bioconductor
updated 22 months ago by
Guido Hooiveld
★ 4.1k • written 2.2 years ago by
cinzia.spagnoli
• 0
0
votes
5
replies
3.0k
views
Gviz: UcscTrack and "GC Percent" information
Gviz
coMET
3.0 years ago • updated 2.2 years ago
Daniel E. Weeks
▴ 30
1
vote
4
replies
6.1k
views
How to process Nimblegen microarray .pair files to get normalized expression matrix
Microarray
Preprocessing
NimbleGen
Normalization
written 3.1 years ago by
Sarah
• 0
1
vote
5
replies
1.6k
views
Mixed up sample info with plotPCA
plotMA
ggplot2
plotPCA
DESeq2
updated 2.2 years ago by
Michael Love
43k • written 2.2 years ago by
sara.jacobson
• 0
2
votes
6
replies
1.6k
views
Biostrings error at retrieving protein sequences
SequenceMatching
Biostrings
DifferentialExpression
Proteome
updated 2.2 years ago by
Hervé Pagès
16k • written 2.2 years ago by
nromerov
• 0
0
votes
4
replies
1.1k
views
Extract LRT results for each comparison
LRT
DESeq2
updated 2.2 years ago by
ATpoint
★ 5.0k • written 2.2 years ago by
Yijing
• 0
0
votes
2
replies
970
views
bug in block.plsda from mixOmics?
mixOmics
2.2 years ago
Lluís Revilla Sancho
▴ 760
0
votes
1
reply
748
views
Is SeqSQC compatible with hg38?
SeqSQC
hg38
updated 2.2 years ago by
James W. MacDonald
68k • written 2.2 years ago by
isml2688
• 0
0
votes
2
replies
2.3k
views
using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
2.2 years ago
Gregory
• 0
0
votes
1
reply
1.1k
views
Comparing RNASeq data from multiple studies
RNASeqData
RnaSeqSampleSize
RNASeqPower
RNASeq
updated 2.2 years ago by
Basti
▴ 780 • written 2.2 years ago by
Luke
• 0
1
vote
1
reply
1.2k
views
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
James W. MacDonald
68k • written 2.2 years ago by
lin.pei26
• 0
1
vote
4
replies
1.5k
views
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
votes
2
replies
2.8k
views
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
votes
1
reply
709
views
error running exp2grn
NewWave
updated 2.2 years ago by
Fabricio Almeida-Silva
▴ 40 • written 2.3 years ago by
adriana
• 0
0
votes
2
replies
880
views
Singlecell protein surface (ADT) pseudotime techniques
monocle
slingshot
2.2 years ago
EspressoKris
▴ 10
0
votes
3
replies
829
views
shinyMethyl - saving the file
shinyMethyl
2.2 years ago
dorota.komar
• 0
2
votes
4
replies
1.6k
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData
DifferentialExpression
SmallRNAData
DESeq2
2.2 years ago
Shihui
• 0
0
votes
3
replies
1.2k
views
Suggested package missing from Development version of Bioconductor
Devel
updated 2.2 years ago by
shepherl
4.2k • written 2.2 years ago by
Richard
• 0
0
votes
0
replies
672
views
mixOmics with Bioconductor classes
mixOmics
2.2 years ago
Lluís Revilla Sancho
▴ 760
0
votes
0
replies
875
views
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
views
Batch effect adjust in model matrix
BatchEffect
edgeR
updated 2.2 years ago by
ATpoint
★ 5.0k • written 2.2 years ago by
Giuseppe
• 0
0
votes
1
reply
706
views
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
Gordon Smyth
53k • written 2.2 years ago by
Jonathan
▴ 10
0
votes
5
replies
1.2k
views
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
James W. MacDonald
68k • written 2.2 years ago by
nilanjanamani88
• 0
46,693 results • Page
41 of 934
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Comment: Question about RE-agnostic mode for intact Hi-C and Micro-C normalization(HiCDCP
by
TikTsoksocissalpc
• 0
Normalizing complex datasets like Hi C can be challenging, much like setting up a PC for optimal gaming performance. Just as careful tuning…
Comment: p.adjust BH Question
by
TikTsoksocissalpc
• 0
Thanks for sharing your question about RMA limma analysis While working on your experiment, it s always helpful to have some background mu…
Answer: NUPOP usage
by
shepherl
4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker?
by
fnfgame
• 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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