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5
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CustomProDB: specify a snp dataset to be used for the SNP annotation
customProDB
51 minutes ago
04.marshal-decibel
• 0
0
votes
0
replies
17
views
I cannot install "microbiome"
GenomeInfoDbData
microbiome
phyloseq
5 hours ago
kikiki
• 0
0
votes
0
replies
14
views
error in function useDataset of biomaRt
bioma
biomaRt
6 hours ago
Riley Qiu
• 0
0
votes
2
replies
120
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils
emptyDrops
scRNA
scRNAseq
10x
updated 6 hours ago by
Aaron Lun
★ 27k • written 5 days ago by
Peter Hickey
▴ 560
2
votes
2
replies
67
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor
fastMNN
scRNAseq
2 days ago • updated 7 hours ago
Guandong Shang
▴ 20
0
votes
4
replies
180
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater
batchelor
scRNAseq
fastMNN
updated 17 hours ago by
Aaron Lun
★ 27k • written 8 days ago by
Guandong Shang
▴ 20
0
votes
2
replies
59
views
How to get started with DeseqDataSet import using CSV? Is it necessary to have ColData command?
Metagenomics
DESeq2
updated 1 day ago by
ATpoint
★ 1.4k • written 1 day ago by
Muhammad
• 0
1
vote
2
replies
83
views
Which is the best type of data for correlation or survival analysis
TPM
RNASeq
RSEM
DESeq2
2 days ago • updated 1 day ago
Yang Shi
• 0
1
vote
1
reply
39
views
How can I do pathway analysis by ChipPeakAnno package?
ChIPpeakAnno
2 days ago
mehdi
• 0
0
votes
3
replies
95
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST
ROntoTools
KEGG
KEGGgraph
2 days ago
abf
▴ 30
3
votes
2
replies
59
views
MEDIPS for chIP-Seq
ChIPSeq
2 days ago
Darek
▴ 10
3
votes
9
replies
369
views
BiocParallel error with ChIPQC
BiocManager
ChIPQC
RSamtools
BiocParallel
7 weeks ago • updated 2 days ago
etiennedanis
• 0
1
vote
1
reply
65
views
Handling heterogeneous data in DESeq2: multiple covariates to control against
RNASeq
DESeq2
updated 2 days ago by
ATpoint
★ 1.4k • written 2 days ago by
seeta_rajpara
• 0
0
votes
3
replies
106
views
Detection of reference genes by Deseq2
lessAbs
reference_genes
DESeq2
updated 51 minutes ago by
ATpoint
★ 1.4k • written 3 days ago by
sj
• 0
4
votes
3
replies
81
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran
Clustering
SingleCellExperiment
annotate
cluster
updated 2 days ago by
James W. MacDonald
60k • written 3 days ago by
achoppe
• 0
1
vote
4
replies
99
views
batch effect
TargetScoreData
batchelor
3 days ago • updated 2 days ago
Syed Zaheer
▴ 10
0
votes
1
reply
50
views
Problem with annotations using annotatr
annotatr
3 days ago
eric.rhoncalderon
• 0
0
votes
0
replies
24
views
MAI error - vector size limit
randomForest
MAI
3 days ago
Hans-Ulrich Klein
▴ 330
1
vote
1
reply
58
views
From KEGG ID's (Kxxxxx) to Uniprot IDs
KEGG
UniProt.ws
updated 3 days ago by
James W. MacDonald
60k • written 4 days ago by
Recep
• 0
0
votes
1
reply
66
views
Rsubread align --R session aborts
RNA
Alignment
Rsubread
updated 3 days ago by
Wei Shi
★ 3.5k • written 4 days ago by
sreekalasn
• 0
0
votes
0
replies
62
views
Job:
BioConductor Tutor $50-$100/Hr
JobPosting
updated 4 days ago by
shepherl
3.2k • written 4 days ago by
Andrew
• 0
1
vote
3
replies
84
views
mapToAlignments_issue
GenomicAlignments
4 days ago • updated 2 days ago
david.porubsky
• 0
1
vote
5
replies
154
views
DESeq2 outlier options and LFC Shrinkage
DESeq2
RNASeq
RnaSeqSampleSize
apeglm
updated 2 days ago by
Michael Love
37k • written 5 days ago by
Riley
• 0
1
vote
1
reply
54
views
Swish: contrasts and interactions
fishpond
DESeq2
updated 5 days ago by
Michael Love
37k • written 5 days ago by
alexyz
• 0
2
votes
4
replies
270
views
edgeR processAmplicons not recognizing hairpin sequences
edgeR
updated 3 days ago by
Gordon Smyth
46k • written 18 days ago by
Claire.Prince
▴ 10
0
votes
1
reply
79
views
Building model matrix to correct for batch effect with biological and technical replicates: Problem with linear correlations
MassSpectrometryData
BatchEffect
r
limma
updated 4 days ago by
Gordon Smyth
46k • written 5 days ago by
mfaleevs
• 0
0
votes
5
replies
571
views
CHIPQC error regarding BiocParallel
CHIPQC
Diffbind
chipseq
rory stark
Thomas Carroll
updated 3 days ago by
arisarkar88
• 0 • written 2.3 years ago by
bioinfouser2
▴ 10
1
vote
2
replies
134
views
Could it be possible to get an older version of ChIPQC?
ChIPQC
ChIP-seq
DiffBind
Rory_Stark
13 days ago • updated 2 days ago
etiennedanis
• 0
0
votes
1
reply
50
views
Extract specific portion of a string and paste to a new column in R
Rscript
tidyr
dataframe
tidyverse
updated 5 days ago by
James W. MacDonald
60k • written 5 days ago by
Nikhil
• 0
2
votes
2
replies
100
views
Contradictory results in smallRNA differential expression analysis using DESeq2
SmallRNA
DESeq2
6 days ago • updated 4 days ago
jucosie
• 0
0
votes
8
replies
198
views
Swish log2FC NA output
swish
fishpond
DifferentialExpression
6 days ago • updated 5 days ago
jvandinter
• 0
1
vote
1
reply
100
views
Dispersion estimates with DESeq2
dispersionestimates
dispersion
DESeq2
estimates
deseq2
updated 6 days ago by
Michael Love
37k • written 10 days ago by
Julia
▴ 10
0
votes
6
replies
234
views
Is DESeq2 generating false postives when changing different pre-filtering thresholds?
RNASeq
DEG
DESeq2
10 days ago • updated 2 days ago
Weiqian
• 0
0
votes
1
reply
146
views
DESeq2 - Batch effect correction in 2 conditions + 2 genotypes + interaction term design
DESeq2
updated 6 days ago by
Michael Love
37k • written 18 days ago by
barbara.mariotti
• 0
0
votes
1
reply
118
views
CQN to DESeq2
cqn
DESeq2
updated 6 days ago by
Michael Love
37k • written 15 days ago by
bioinfo
• 0
0
votes
0
replies
39
views
Can I loosely say that a gene is expressed by simply look at the gene count from RNA-Seq?
RNASeqData
RNASeq
6 days ago
Pang
• 0
0
votes
1
reply
51
views
Error in running: classifySingleR from SingleR package
SingleR
SingleCell
updated 6 days ago by
ATpoint
★ 1.4k • written 6 days ago by
amit.korngut
• 0
0
votes
1
reply
61
views
MBD-seq non model species
MethylSeq
ramwas
MEDIPS
qsea
updated 6 days ago by
Guillaume Devailly
▴ 40 • written 6 days ago by
Marianna
• 0
1
vote
1
reply
85
views
Filtering Orthologus Genes Before or After TMM normalization?
RNASeq
Normalization
TMM
edgeR
updated 6 days ago by
Gordon Smyth
46k • written 6 days ago by
e.g.w.miller
▴ 10
1
vote
5
replies
158
views
what should be our references when 2 samples which I compare are treated and there is not any control?
DESeq2
updated 2 days ago by
Michael Love
37k • written 6 days ago by
Maryam.sed1400
• 0
4
votes
4
replies
174
views
Convert an R data.frame to a bed file in R
rtracklayer
R
bed
9 days ago • updated 5 days ago
L
• 0
0
votes
2
replies
91
views
Differences in ENSEMBL => ENTREZID mapping coverage between org.Hs.eg.db and AnnotationHub resources
AnnotationHub
org.Hs.eg.db
ensembldb
updated 6 days ago by
James W. MacDonald
60k • written 8 days ago by
sandmann.t
▴ 70
0
votes
0
replies
42
views
Job:
Bioinformatics Analyst (non-PhD level) in medical science
JobPosting
6 days ago
zhen-fu
• 0
0
votes
2
replies
67
views
MAAPER
MAAPER
updated 6 days ago by
ATpoint
★ 1.4k • written 6 days ago by
Sasha
• 0
0
votes
1
reply
84
views
I have a query regarding differential gene expression using limma-voom.
RNASeqData
DESeq2
updated 7 days ago by
Gordon Smyth
46k • written 7 days ago by
btadfaramin
• 0
1
vote
4
replies
668
views
xcmsRaw not reading data files in: invalid class “xcmsFileSource” object
xcms
updated 7 days ago by
jiahui
• 0 • written 21 months ago by
garfield320
▴ 30
9
votes
21
replies
11k
views
ah <- AnnotationHub() Error in UseMethod("filter_"): no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tb…
AnnotationHub
dplyr
updated 8 days ago by
SmallChess
▴ 10 • written 21 months ago by
georgia.katsoula
▴ 40
0
votes
0
replies
89
views
Job:
Scientific Programmer | Altos Labs | San Diego
SpatialData
scRNAseq
JobPosting
8 days ago • updated 6 days ago
peter.kharchenko
▴ 30
0
votes
1
reply
116
views
End User Agreement License
licensing
updated 8 days ago by
sandmann.t
▴ 70 • written 11 days ago by
mgardner
• 0
0
votes
1
reply
85
views
APAanalyzer
APAlyzer
8 days ago • updated 6 days ago
Sasha
• 0
42,915 results • Page
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Comment: Detection of reference genes by Deseq2
by
ATpoint
★ 1.4k
Long story short, use `plotMA()` to see how normalization went. If the plot is somewhat symmetric and/or the majority of point center along…
Comment: how to do downstram analysis to cells which are subsetted after MNN batch-correc
by
Guandong Shang
▴ 20
Thanks for your reply, Aaron :)
Answer: `emptyDrops()` calling 'too many' non-empty droplets
by
Aaron Lun
★ 27k
Perhaps there is something wonky with the TCR sequences that exclude them from the barcodes with below 100 counts. Maybe TCR sequences are …
Answer: how to do downstram analysis to cells which are subsetted after MNN batch-correc
by
Aaron Lun
★ 27k
In this case, you can just replace `denoisePCA` in the example with the various MNN steps. So: ``` # NOTE: not tested! sce.sub <- sce[…
Answer: how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more rea
by
Aaron Lun
★ 27k
It is, in general, difficult to interpret the `reconstructed` assay, as batch correction is not guaranteed to do "sensible" things to the p…
Votes
Answer: how to do downstram analysis to cells which are subsetted after MNN batch-correc
Answer: how to do downstram analysis to cells which are subsetted after MNN batch-correc
Comment: SingleCellExperiment: Edit cluster IDs in colLabels
Comment: what should be our references when 2 samples which I compare are treated and the
Comment: Which is the best type of data for correlation or survival analysis
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