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monocle
•
reset
0
votes
2
replies
224
views
A problem occurs when running the monocle2
monocle
written 12 weeks ago by
yuheng_yang
• 0
1
vote
1
reply
1.1k
views
Differentially expressed genes in monocle pseudotime
monocle
updated 20 months ago by
Gordon Smyth
53k • written 20 months ago by
kthapa
• 0
0
votes
2
replies
870
views
Singlecell protein surface (ADT) pseudotime techniques
monocle
slingshot
2.2 years ago
EspressoKris
▴ 10
0
votes
0
replies
900
views
weighting sample group
monocle
SingleCell
DifferentialExpression
3.2 years ago
Sogand
• 0
2
votes
4
replies
3.9k
views
Trajectory analysis for single cell sequencing
single cell
trajectory analysis
tscan
monocle
updated 5.3 years ago by
Aaron Lun
★ 29k • written 5.3 years ago by
lirongrossmann
▴ 50
0
votes
1
reply
4.2k
views
How to customize the color in 'plot_cell_trajectory' function
scRNA seq
monocle
updated 5.4 years ago by
Kevin Blighe
★ 4.0k • written 5.4 years ago by
initialqy
• 0
0
votes
1
reply
3.6k
views
Pseudotime analysis on bulk RNASeq using monocle
pseudotime
monocle
dimensionality
5.9 years ago
pbachali
▴ 50
0
votes
1
reply
6.4k
views
monocle error at orderCells
scRNA
monocle
packages
Tutorial
6.3 years ago
444579004
• 0
5
votes
3
replies
2.1k
views
Setting gene expression thresholds for trajectory analysis using Monocle
monocle
differential gene expression
detectgenes function
Tutorial
6.9 years ago
S.Webb6
▴ 40
1
vote
1
reply
3.4k
views
Mean Expression Calculation scRNA-seq (All cells or only Expressed Cells)
scrnaseq
monocle
updated 7.6 years ago by
davide risso
▴ 980 • written 7.6 years ago by
chitsazanalex
▴ 10
0
votes
1
reply
2.1k
views
Converting scater-normalized UMI data to Monocle CellDataSet
scater
scran
umi
monocle
updated 7.6 years ago by
Aaron Lun
★ 29k • written 7.6 years ago by
supremerulersuraj
• 0
0
votes
1
reply
2.5k
views
monocle: Error in if (cds@expressionFamily@vfamily %in% c("negbinomial", "negbinomial.size"))
monocle
7.8 years ago
Mehmet Ilyas Cosacak
• 0
1
vote
5
replies
3.3k
views
Monocle causes R session to crash
software error
monocle
updated 8.4 years ago by
kevin.rue
▴ 350 • written 10.1 years ago by
galib36
▴ 10
0
votes
0
replies
1.9k
views
Documentation of "branch_states" and "branch_labels" arguments
monocle
8.4 years ago
kevin.rue
▴ 350
0
votes
0
replies
3.4k
views
Monocle plot_pseudotime_heatmap : Error in cutree(tree, cutree_n) : elements of 'k' must be between 1 and 3
R
monocle
8.4 years ago
A.H
• 0
3
votes
1
reply
1.5k
views
Normalizing vs RNA content in scRNAseq data
monocle
scran
updated 8.4 years ago by
Aaron Lun
★ 29k • written 8.4 years ago by
ankur.chakravarthy.10
▴ 40
0
votes
3
replies
1.8k
views
Batch effects and model matrices
deseq2
single cell
monocle
updated 8.5 years ago by
Michael Love
43k • written 8.5 years ago by
bvernot
• 0
0
votes
0
replies
1.4k
views
Basic Question: How to get appropriate pDATA structure in monocle from cufflinks/cuffnorm
cufflinks
monocle
8.5 years ago
alexandriapinto1
▴ 10
0
votes
1
reply
1.5k
views
Monocle group sizes
monocle
8.7 years ago
ribioinfo
▴ 100
0
votes
1
reply
4.1k
views
error in monocle.
monocle
updated 8.7 years ago by
driver.ian
• 0 • written 8.7 years ago by
ikwak
• 0
0
votes
0
replies
2.2k
views
Monocle-strange differential expression results
monocle
differential expression
9.9 years ago
sunil.mangalam
• 0
0
votes
0
replies
1.8k
views
error: no slot of name "expressionFamily" for this object of class "CellDataSet"
monocle
bugs
10.1 years ago
wanghao1993333
• 0
1
vote
2
replies
2.2k
views
Error message running DE-test in Monocle
monocle
cummerbund
DE
rnaseq
updated 10.4 years ago by
ksekine
• 0 • written 10.7 years ago by
Jon Bråte
▴ 270
23 results • Page
1 of 1
Recent ...
Replies
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…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
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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