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0
replies
912
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Possible to customize the parallel computation used in readGAlignments?
R
readGAlignments
GenomicAlignments
3.2 years ago
chen_ying
▴ 10
0
votes
0
replies
1.3k
views
Gene co-expression network analysis with small sample size
Network
3.2 years ago
Senthil
• 0
0
votes
0
replies
1.2k
views
Edit alignment in msa
alig
msa
Alignment
3.2 years ago
Luis
• 0
0
votes
1
reply
1.2k
views
' Update all/some/none? [a/s/n]: '
forensic
expt
updated 3.2 years ago by
tomhenry099
• 0 • written 3.2 years ago by
attia
• 0
0
votes
3
replies
1.8k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy
scRNAseq
fastmnn
r
3.2 years ago
Madiha
• 0
0
votes
1
reply
1.1k
views
I want to convert the go enrichment result to a data frame (tidy data)with two column which one is the gene symbol and the other is go term. Any one…
GO.db
GOfuncR
GO
GOSim
goProfiles
updated 3.2 years ago by
Basti
▴ 780 • written 3.2 years ago by
yeluo
• 0
0
votes
0
replies
698
views
GenVisR - adding on genomic positions to CovGen graph
GenVisR
GenCov
3.2 years ago
Amy_
• 0
0
votes
0
replies
864
views
Gene Ontology on Streptococcus Pneumoniae genes sets
GO
GeneOntology
LocusIDtogeneIDconversion
3.2 years ago
BioinFo.X
• 0
0
votes
0
replies
548
views
H bond prediction of two sequences
GeneMeta
generegulation
3.2 years ago
Marcus
• 0
1
vote
0
replies
1.4k
views
adjusted p-values with topGO elim.KS method
topGO
Ontology
DifferentialExpression
3.2 years ago
Kevin Gregory
▴ 10
0
votes
1
reply
2.7k
views
Treeplot by enrichplot
clusterProfiler
enrichplot
treeplot
updated 3.2 years ago by
Guangchuang Yu
★ 1.2k • written 3.3 years ago by
g.neri19
• 0
0
votes
0
replies
957
views
question on the p value for VIPER results by dorothea
RNAseq
VIPER
Doth
3.3 years ago
snowmattin
• 0
0
votes
0
replies
977
views
Outliers
Proteomics
Proteome
updated 3.2 years ago by
ATpoint
★ 5.0k • written 3.3 years ago by
bansalheena10
• 0
0
votes
0
replies
1.6k
views
HISAT2 and HTSEQ command
HTSeqGenie
3.3 years ago
Maryam.sed1400
• 0
0
votes
0
replies
1.2k
views
WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network
Transcriptomics
MicrobiomeData
RNASEQ
WCGNA
3.3 years ago
Julieta
• 0
2
votes
1
reply
1.3k
views
WGCNA: weird issue of module with a single gene
network
co-expression
WGCNA
updated 3.3 years ago by
andres.firrincieli
▴ 50 • written 3.3 years ago by
ikumar2000
▴ 10
0
votes
0
replies
910
views
weighting sample group
monocle
SingleCell
DifferentialExpression
3.3 years ago
Sogand
• 0
0
votes
0
replies
1.4k
views
Simplify - clusterProfiler
RNASeq
simplify
clusterProfiler
enrichGO
simplifyEnrichment
3.3 years ago
estafana.t98
• 0
0
votes
2
replies
1.4k
views
Error message from protein coding prediction with VariantAnnotation
R
VariantAnnotation
3.3 years ago
rwan.work
• 0
1
vote
1
reply
1.3k
views
Confused about design for RNA seq experiment
RNAseq
ExperimentData
RNAseq123
RNA
ExperimentalDesign
updated 3.3 years ago by
ATpoint
★ 5.0k • written 3.3 years ago by
Mohamed
▴ 30
0
votes
0
replies
609
views
Identification of tissue-specific exons using DEXSeq
#Retina
#RNA-Seq
#DEXSeq
3.3 years ago
osieman52
• 0
0
votes
0
replies
763
views
how to create PHENO_DATA
RNASeq
RNASeqData
RNASeqRData
3.3 years ago
marymshahi2021
• 0
0
votes
2
replies
1.6k
views
Error when using tallyVariants with parallel jobs not returning results
VariantTools
updated 3.3 years ago by
Vincent J. Carey, Jr.
6.7k • written 3.3 years ago by
Imraan
• 0
1
vote
0
replies
894
views
Data format format for summarising each NGS read without collapsing into a count
DataRepresentation
exSTRa
Rsamtools
3.3 years ago
Rick
▴ 10
0
votes
1
reply
2.4k
views
[ NEED HELP >:( ] ggtree Installation Error
ggtree
updated 3.3 years ago by
shepherl
4.2k • written 3.3 years ago by
Muhammad Isa
• 0
1
vote
1
reply
1.7k
views
issue with biomaRt ENSEMBL_MART_SNP
biomaRt
updated 3.3 years ago by
Mike Smith
★ 6.6k • written 3.3 years ago by
Laurel
▴ 10
0
votes
0
replies
745
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
3.3 years ago
Matthias Munz
▴ 20
0
votes
0
replies
773
views
GO-terms Semantic Similarity Measures: How to decide which method(s) to use?
SemanticSimilarityMeasures
GO-terms
3.3 years ago
Andrew
• 0
0
votes
0
replies
920
views
Finding DEGs between two different datasets using limma
Proteomics
limma
proteomi
3.3 years ago
mfaleevs
• 0
0
votes
2
replies
2.6k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
FeatureCounts
3.3 years ago
KMS
▴ 20
0
votes
5
replies
3.1k
views
How to add a BioConductor package to a Docker image based on rocker/shiny
docker
3.3 years ago
Sam
▴ 10
1
vote
3
replies
3.1k
views
read.bismark() ->Error in manager$availability[[as.character(result$node)]] <- TRUE : wrong args for environment subassignment
methylSig
bsseq
updated 3.3 years ago by
Peter Hickey
▴ 760 • written 3.3 years ago by
carla.geiger
• 0
0
votes
0
replies
1.2k
views
Query on TCGA
TCGAbiolinks
TCGAWorkflow
3.3 years ago
hemangininaik09
• 0
0
votes
0
replies
1.8k
views
Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array
SingleCellExperiment
DelayedArray
3.3 years ago
merv
▴ 150
1
vote
4
replies
1.5k
views
Error of PWM not colsum to 1 from package DiffLogo or seqLogo
seqLogo
DiffLogo
3.3 years ago
zhxiaokang
▴ 20
0
votes
1
reply
1.1k
views
getBM Error with certain attribute combinations
biomaRt
ensembldb
updated 3.3 years ago by
ATpoint
★ 5.0k • written 3.3 years ago by
Luisa
• 0
0
votes
0
replies
1.6k
views
Error in GDCDownload and GDCPrepare for TCGA-PAAD Dataset
GDCPrepare
GDCDownload
3.3 years ago
Manav
• 0
0
votes
0
replies
821
views
Tuning the MetaVolcanoR plots
limma
MetaVolcanoR
3.3 years ago
JAcky
• 0
0
votes
0
replies
840
views
maSigPro visualizing individually each plot from each cluster
plot
maSigPro
Clustering
3.3 years ago
oseias.rf.junior
• 0
1
vote
1
reply
1.4k
views
Unable to install "scruff" with BiocManager::install()
scruff
Install
ShortRead
updated 3.3 years ago by
shepherl
4.2k • written 3.3 years ago by
Jackson
• 0
0
votes
2
replies
2.1k
views
long computing time for TSS enrichment score
ATACSeq
updated 2.3 years ago by
Noah
• 0 • written 3.3 years ago by
Taeim
• 0
0
votes
1
reply
1.7k
views
WGCNA - Network construction and module detection
gene
Clustering
wgcna
flashclust
updated 3.3 years ago by
andres.firrincieli
▴ 50 • written 3.3 years ago by
Recep
▴ 20
0
votes
2
replies
1.7k
views
getSRAdbFile() does not work
SRAdb
GEOmetadb
3.3 years ago
jfertaj
▴ 30
0
votes
1
reply
2.5k
views
Complex Heatmap - correlation matrix - how to have exact same annotation with same colors for rows and columns?
R
heatmaps
ComplexHeatmap
Heatma
updated 3.3 years ago by
Zuguang Gu
▴ 290 • written 3.3 years ago by
תום
• 0
0
votes
0
replies
1.1k
views
Cluster profiler - adj p-value differ from Enrichr
clusterProfiler
enrichR
3.3 years ago
angkoo
▴ 10
4
votes
6
replies
2.5k
views
HTSeq command option for single-end reads
HTSeqGenie
3.3 years ago
Maryam.sed1400
• 0
0
votes
1
reply
1.4k
views
How does MAST caculate log fc
MAST
3.3 years ago • updated 6 months ago
Chenghao
▴ 10
0
votes
3
replies
2.2k
views
using of z score in Differentially Expression Analysis
RNASeqR
updated 3.3 years ago by
ATpoint
★ 5.0k • written 3.3 years ago by
fatemehfakhari74
• 0
0
votes
1
reply
998
views
Interpret MetaVolcanoR plot
MetaVolcanoR
updated 3.3 years ago by
Kevin Blighe
★ 4.0k • written 3.3 years ago by
JAcky
• 0
0
votes
2
replies
1.5k
views
Microbiome 16S amplicon analysis in dada2
bioinformatics
DADA2
3.3 years ago
anasjamshed1994
• 0
1,000 results • Page
18 of 20
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Answer: Question about RE-agnostic mode for intact Hi-C and Micro-C normalization(HiCDCP
by
victor04052024
• 0
You write quite well, and the content is very interesting. I'll provide you a link to my page [granny 2](https://granny2.io).
Answer: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
by
victor04052024
• 0
The information is interesting, and your writing is excellent. I will provide you a link to my website [Baseball bros](https://baseball-gam…
Comment: segfault in edgeR glmQLFit
by
Gordon Smyth
53k
We have committed a bug fix now to edgeR on both the release and developmental Bioconductor repositories.
Answer: Ensembl site unresponsive via biomaRt
by
horaortiz8
• 0
I appreciate the link. I'll get in touch with them directly; I wish they had a status page of some kind. https://www.ensembl.org/Help/Cont…
Comment: segfault in edgeR glmQLFit
by
Mark
• 0
Thanks! We had been considering some of these adjustments as well, given the small number of features and total reads. Your advice is well-…
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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