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0
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1.0k
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Can ChiPseeker be as highly customizable as "computeMatrix"? for example if I want to plot the distribution of genes on the TAD boundary?
deeptools
ChIPseeker
2.8 years ago
840842906
• 0
0
votes
0
replies
580
views
Single Series Time Course
tissueTreg
2.8 years ago
guang-hui
• 0
0
votes
0
replies
875
views
data truncation with sce2fcs()
CATALYST
2.8 years ago
Shaun
• 0
0
votes
0
replies
467
views
How to draw the MEM matrix of cell annotation
MatrixDiagram
2.8 years ago
shuangshuang
• 0
0
votes
1
reply
946
views
Microarray Data - Matching Probe ID's to Gene Expression Symbols
limma
updated 2.8 years ago by
Kevin Blighe
★ 4.0k • written 2.8 years ago by
Joshua
• 0
1
vote
3
replies
1.9k
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler
RNASeq
updated 20 months ago by
Guangchuang Yu
★ 1.2k • written 2.8 years ago by
ruiqi.li
▴ 10
0
votes
0
replies
1.1k
views
How to find regulatory region position and associated genes for CpG sites
Epigenetics
R
Bioconducter
2.8 years ago
Jitendra
▴ 10
0
votes
2
replies
1.9k
views
How to use the plotExprHeatmap function to draw heat maps according to groups
grou
heatmaps
CyTOFpower
cytofWorkflow
2.8 years ago
shuangshuang
• 0
0
votes
0
replies
773
views
Coloring reads in AlignmentsTrack based on mapq
Gviz
2.8 years ago
Vinicius Henrique da Silva
▴ 40
0
votes
3
replies
2.4k
views
Knee and Inflection of DropletUtils
SingleCell
updated 2.8 years ago by
ATpoint
★ 5.0k • written 2.8 years ago by
ankuuu
• 0
0
votes
1
reply
716
views
Reference categories for factors
assocTestSingle
GENESIS
written 2.9 years ago by
SuperD
• 0
2
votes
6
replies
4.9k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG
clusterProfiler
updated 23 months ago by
Guido Hooiveld
★ 4.1k • written 2.8 years ago by
ruiqi.li
▴ 10
0
votes
0
replies
832
views
MAST for single cell ATAC data
MAST
2.8 years ago
zuljiamel1991
▴ 10
1
vote
2
replies
2.7k
views
Error when running GDC_prepare
TCGAbiolinks
2.8 years ago
DevelopingHippo
• 0
0
votes
0
replies
820
views
Merging 2 staining panels
FlowCytometry
flowCore
2.8 years ago
michaela.gregorova13
• 0
0
votes
0
replies
1.2k
views
Aligning Clariom D against reference Genome and transcriptome pipeline
Clariom
Align
MicroarrayData
Alignment
Microarray
2.8 years ago
agamemnon
• 0
0
votes
0
replies
662
views
Pipeline error
ramwas
bams
updated 2.8 years ago by
James W. MacDonald
68k • written 2.8 years ago by
Anushka
• 0
0
votes
3
replies
2.1k
views
batch effect in EPIC array data
statistics
Epigenetics
R
updated 2.8 years ago by
Lluís Revilla Sancho
▴ 760 • written 2.8 years ago by
Jitendra
▴ 10
0
votes
0
replies
911
views
How to draw module significance barplot?
module_significance
barplot
WGCNA
2.8 years ago
Sooni
▴ 10
5
votes
2
replies
1.3k
views
outdated GEOmetadb.sqlite
GEOmetadb
2.8 years ago • updated 23 months ago
Robert Castelo
★ 3.4k
0
votes
1
reply
1.7k
views
Error: all(unlist(md_cols) %in% names(md)) is not TRUE
cytofWorkflow
updated 2.8 years ago by
helucro
▴ 70 • written 2.8 years ago by
shuangshuang
• 0
0
votes
1
reply
823
views
maxfragmentsize problem
ramwas
ram
updated 2.8 years ago by
ATpoint
★ 5.0k • written 2.8 years ago by
Anushka
• 0
0
votes
1
reply
739
views
Log of Step 1
log
timer
updated 2.8 years ago by
ATpoint
★ 5.0k • written 2.8 years ago by
Anushka
• 0
0
votes
1
reply
842
views
Rbam and Rqc files error
Rqc
rbams
rqc
mmusculus
scanbams
updated 2.8 years ago by
ATpoint
★ 5.0k • written 2.8 years ago by
Anushka
• 0
0
votes
0
replies
653
views
how to convert lncRNA probe name or mRNA probe name to gene symbol
lncRNA
probeID
mRNA
genesymbol
2.8 years ago
Sooni
▴ 10
1
vote
2
replies
1.9k
views
GO.db for Bioconductor 3.17
GO.db
devel
2.8 years ago
Amanda D. Clark
• 0
0
votes
0
replies
794
views
some questions about eliminating efficiency biaes in csaw user's guide
csawUsersGuide
csaw
2.8 years ago
sashu
• 0
0
votes
0
replies
1.2k
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread
GTF
featureCounts
segmentationfault
2.8 years ago
yao hua
• 0
6
votes
12
replies
3.1k
views
Error when loading DMRcate
DMRcate
2.8 years ago
Bazingastats
• 0
0
votes
1
reply
1.7k
views
part of the volcano plot does not appear.
plot
volcano
volcanoplot
updated 2.8 years ago by
Basti
▴ 780 • written 2.8 years ago by
Sooni
▴ 10
0
votes
0
replies
1.4k
views
Problem with loading rtracklayer
rtracklayer
updated 2.8 years ago by
shepherl
4.2k • written 2.8 years ago by
jiahe.janet
• 0
0
votes
1
reply
1.0k
views
Installation of SingleR fails with GCC 8.2.0, Centos 7 - XPtr(Rcpp::Vector<19>::Proxy)
SimpleR
updated 2.7 years ago by
Jovana Maksimovic
▴ 20 • written 2.8 years ago by
cisbio
• 0
0
votes
0
replies
979
views
VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf
AS_SB_TABLE
readVcf
Mutect2
VariantAnnotation
2.8 years ago
therealgenna
• 0
0
votes
0
replies
766
views
XCMS normalization
xcms
2.8 years ago
T.RU
• 0
0
votes
0
replies
881
views
Multiple way network preservation
wgcna
2.8 years ago
madzayasodara
• 0
0
votes
14
replies
3.4k
views
Trouble downloading dada2
dada
dada2
2.8 years ago
elliottchon97
• 0
0
votes
0
replies
789
views
Dereplicate DNA sequences while taking into account the corresponding taxonomy
Biostrings
2.8 years ago
Gilles
• 0
1
vote
2
replies
1.6k
views
snpsBySeqname() and snpsByOverlaps() functions in BSgenome package did not work in my computer
BSgeome
2.8 years ago
sunyingkai
• 0
0
votes
0
replies
1.2k
views
DMR.plot "Error: Too many stacks to draw"
DMRcate
Gviz
GV
2.8 years ago
gilliangoobie
• 0
0
votes
0
replies
653
views
Visualize blastx output in R
blast
2.8 years ago
kvigil
• 0
0
votes
0
replies
676
views
installing flowPloidy
flowPloidyData
flowPloidy
2.8 years ago
Punn
• 0
0
votes
0
replies
1.2k
views
BiomaRt - Problem to access homolog lists
biomaRt
ensembldb
2.8 years ago
ginie.dub
• 0
0
votes
4
replies
1.2k
views
Load templates from openPrimeR
PCRmultiplex
openPrimeR
2.9 years ago • updated 2.8 years ago
Santiago Edilberto
• 0
0
votes
0
replies
781
views
Using MBD score in MBD-seq
mbd-seq
MethylSeq
2.9 years ago
Marianna
▴ 20
0
votes
0
replies
983
views
WGCNA TOM file empty
WGCNA
TOM
2.9 years ago
gianni.drm
• 0
0
votes
0
replies
838
views
Rsamtools pileup help
Rsamtools
pileup
2.9 years ago
JoeMG
• 0
1
vote
1
reply
1.2k
views
GoSemSim - function mgeneSim() is resulting in similarity matrix without 1s on diagonal
GOSim
GOSemSim
updated 2.8 years ago by
Lluís Revilla Sancho
▴ 760 • written 2.9 years ago by
eliska.ochodkova
▴ 10
1
vote
4
replies
1.3k
views
Genomics data
mygene
offtopic
updated 2.9 years ago by
James W. MacDonald
68k • written 2.9 years ago by
Shila
• 0
0
votes
0
replies
1.2k
views
write.FCS() produces files which cannot be opened by CytExpert software
flowCore
2.9 years ago
pawel.malecki
• 0
0
votes
0
replies
1.6k
views
WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape
Heatmap
heatmaps
WGCNA
2.9 years ago
gianni.drm
• 0
1,000 results • Page
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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()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
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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