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monocle
•
reset
5
votes
3
replies
1.4k
views
Setting gene expression thresholds for trajectory analysis using Monocle
monocle
differential gene expression
detectgenes function
Tutorial
5.3 years ago
S.Webb6
▴ 40
3
votes
1
reply
1.1k
views
Normalizing vs RNA content in scRNAseq data
monocle
scran
updated 6.8 years ago by
Aaron Lun
★ 28k • written 6.8 years ago by
ankur.chakravarthy.10
▴ 40
1
vote
5
replies
2.5k
views
Monocle causes R session to crash
software error
monocle
updated 6.8 years ago by
kevin.rue
▴ 350 • written 8.5 years ago by
galib36
▴ 10
1
vote
1
reply
162
views
Differentially expressed genes in monocle pseudotime
monocle
updated 10 days ago by
Gordon Smyth
50k • written 12 days ago by
kthapa
• 0
1
vote
2
replies
1.7k
views
Error message running DE-test in Monocle
monocle
cummerbund
DE
rnaseq
updated 8.8 years ago by
ksekine
• 0 • written 9.0 years ago by
Jon Bråte
▴ 250
1
vote
4
replies
2.1k
views
Trajectory analysis for single cell sequencing
single cell
trajectory analysis
tscan
monocle
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
lirongrossmann
▴ 40
1
vote
1
reply
2.0k
views
Mean Expression Calculation scRNA-seq (All cells or only Expressed Cells)
scrnaseq
monocle
updated 6.0 years ago by
davide risso
▴ 950 • written 6.0 years ago by
chitsazanalex
▴ 10
0
votes
0
replies
2.5k
views
Monocle plot_pseudotime_heatmap : Error in cutree(tree, cutree_n) : elements of 'k' must be between 1 and 3
R
monocle
6.8 years ago
A.H
• 0
0
votes
0
replies
1.4k
views
Documentation of "branch_states" and "branch_labels" arguments
monocle
6.8 years ago
kevin.rue
▴ 350
0
votes
1
reply
1.7k
views
monocle: Error in if (cds@expressionFamily@vfamily %in% c("negbinomial", "negbinomial.size"))
monocle
6.2 years ago
Mehmet Ilyas Cosacak
• 0
0
votes
1
reply
1.5k
views
Converting scater-normalized UMI data to Monocle CellDataSet
scater
scran
umi
monocle
updated 6.0 years ago by
Aaron Lun
★ 28k • written 6.0 years ago by
supremerulersuraj
• 0
0
votes
1
reply
4.6k
views
monocle error at orderCells
scRNA
monocle
packages
Tutorial
4.7 years ago
444579004
• 0
0
votes
1
reply
2.3k
views
Pseudotime analysis on bulk RNASeq using monocle
pseudotime
monocle
dimensionality
4.3 years ago
pbachali
▴ 50
0
votes
1
reply
2.9k
views
How to customize the color in 'plot_cell_trajectory' function
scRNA seq
monocle
updated 3.8 years ago by
Kevin Blighe
★ 3.9k • written 3.8 years ago by
initialqy
• 0
0
votes
0
replies
450
views
weighting sample group
monocle
SingleCell
DifferentialExpression
19 months ago
Sogand
• 0
0
votes
2
replies
331
views
Singlecell protein surface (ADT) pseudotime techniques
monocle
slingshot
7 months ago
EspressoKris
▴ 10
0
votes
0
replies
1.4k
views
error: no slot of name "expressionFamily" for this object of class "CellDataSet"
monocle
bugs
8.4 years ago
wanghao1993333
• 0
0
votes
0
replies
1.8k
views
Monocle-strange differential expression results
monocle
differential expression
8.3 years ago
sunil.mangalam
• 0
0
votes
1
reply
3.5k
views
error in monocle.
monocle
updated 7.1 years ago by
driver.ian
• 0 • written 7.1 years ago by
ikwak
• 0
0
votes
1
reply
1.1k
views
Monocle group sizes
monocle
7.1 years ago
ribioinfo
▴ 100
0
votes
0
replies
1.0k
views
Basic Question: How to get appropriate pDATA structure in monocle from cufflinks/cuffnorm
cufflinks
monocle
6.9 years ago
alexandriapinto1
▴ 10
0
votes
3
replies
1.3k
views
Batch effects and model matrices
deseq2
single cell
monocle
updated 6.9 years ago by
Michael Love
41k • written 6.9 years ago by
bvernot
• 0
22 results • Page
1 of 1
Recent ...
Replies
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
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