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David Parichy
Apr 23
cds exports and DE weirdness
Hi folks, Two questions (I'm trying not to pester Lauren Saunders as she gets her lab up and
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cds exports and DE weirdness
Hi folks, Two questions (I'm trying not to pester Lauren Saunders as she gets her lab up and
Apr 23
Global Psychedelic
Apr 23
WHERE TO BUY THE BEST CHOCOLATE BARS ONLINE SAFELY IN CHICAGO
Mushrooms contain macronutrients that support a healthy immune system. According to the Mushroom
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WHERE TO BUY THE BEST CHOCOLATE BARS ONLINE SAFELY IN CHICAGO
Mushrooms contain macronutrients that support a healthy immune system. According to the Mushroom
Apr 23
Global Psychedelic
Apr 23
WHERE TO BUY THE BEST GOLDEN TEACHER ONLINE SAFELY IN NEW YORK
Mushrooms contain macronutrients that support a healthy immune system. According to the Mushroom
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WHERE TO BUY THE BEST GOLDEN TEACHER ONLINE SAFELY IN NEW YORK
Mushrooms contain macronutrients that support a healthy immune system. According to the Mushroom
Apr 23
Global Psychedelic
Apr 23
WHERE TO BUY THE BEST MIX AND MATCH D9 EDIBLES ONLINE SAFELY IN ALASKA
Mushrooms contain macronutrients that support a healthy immune system. According to the Mushroom
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WHERE TO BUY THE BEST MIX AND MATCH D9 EDIBLES ONLINE SAFELY IN ALASKA
Mushrooms contain macronutrients that support a healthy immune system. According to the Mushroom
Apr 23
Global Psychedelic
Apr 23
WHERE TO BUY THE BEST POLKADO BARS ONLINE SAFELY IN NEW JERSEY
Mushrooms contain macronutrients that support a healthy immune system. According to the Mushroom
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WHERE TO BUY THE BEST POLKADO BARS ONLINE SAFELY IN NEW JERSEY
Mushrooms contain macronutrients that support a healthy immune system. According to the Mushroom
Apr 23
Global Psychedelic
Apr 23
WHERE TO BUY THE BEST 3 GRAMS RUNTZ DISPOSABLE VAPES ONLINE SAFELY IN DALLAS TEXAS
Mushrooms contain macronutrients that support a healthy immune system. According to the Mushroom
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WHERE TO BUY THE BEST 3 GRAMS RUNTZ DISPOSABLE VAPES ONLINE SAFELY IN DALLAS TEXAS
Mushrooms contain macronutrients that support a healthy immune system. According to the Mushroom
Apr 23
Sanskriti Dey
Apr 8
Error: estimateDispersions only works, and is only needed, when you're using a CellDataSet with a negbinomial or negbinomial.size expression family
hie i want to use monocle 2 for my seurat object but encounter an error Error in .local(object, ...)
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Error: estimateDispersions only works, and is only needed, when you're using a CellDataSet with a negbinomial or negbinomial.size expression family
hie i want to use monocle 2 for my seurat object but encounter an error Error in .local(object, ...)
Apr 8
Riya Keshri
, …
Aastha Pal
3
Apr 2
Preprocess step issue
Hi, I tried installing irlba and matrix, still no luck. Any advice? Thank you, Aastha On Tuesday,
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Preprocess step issue
Hi, I tried installing irlba and matrix, still no luck. Any advice? Thank you, Aastha On Tuesday,
Apr 2
Jean-Baptiste Dupont
,
Aastha Pal
2
Apr 2
Error in preprocess_cds() function
Hi, Were you able to fix this? Thank you, Aastha On Thursday, November 30, 2023 at 12:55:12 AM UTC-8
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Error in preprocess_cds() function
Hi, Were you able to fix this? Thank you, Aastha On Thursday, November 30, 2023 at 12:55:12 AM UTC-8
Apr 2
AP
2
Apr 1
How to get the cell barcodes for Y_ etc ?
I would like to expand this question if it wasn't clear. Basically when I label principal nodes I
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How to get the cell barcodes for Y_ etc ?
I would like to expand this question if it wasn't clear. Basically when I label principal nodes I
Apr 1
Gabriele Zoppoli
, …
Nabil Rahiman
4
Mar 28
Error in graph.adjacency.dense(adjmatrix, mode = mode, weighted = weighted, : At vendor/cigraph/src/constructors/adjacency.c:538 : Adjacency matrix should be symmetric to produce an undirected graph. Invalid value
even the code example from R documentation also didn't work, cell_metadata <- readRDS(system.
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Error in graph.adjacency.dense(adjmatrix, mode = mode, weighted = weighted, : At vendor/cigraph/src/constructors/adjacency.c:538 : Adjacency matrix should be symmetric to produce an undirected graph. Invalid value
even the code example from R documentation also didn't work, cell_metadata <- readRDS(system.
Mar 28
AP
Mar 27
How can I add the trajectory lines on top of Seurat FeaturePlot?
Hi all, I have my trajectories for different subsets of my data and for a given subset the plot_cells
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How can I add the trajectory lines on top of Seurat FeaturePlot?
Hi all, I have my trajectories for different subsets of my data and for a given subset the plot_cells
Mar 27
Matt J
Mar 13
conversion from SCE to CDS
Hey all, I am wanting to use Monocle3 to analyze Cytof data. I was wondering if there is a way to
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conversion from SCE to CDS
Hey all, I am wanting to use Monocle3 to analyze Cytof data. I was wondering if there is a way to
Mar 13
Amelie Raz
2
Jan 31
Where are the UMAP embeddings stashed in the cds object?
Nevermind, I figured it out! It's at cds@int_colData$reducedDims$UMAP On Wednesday, January 31,
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Where are the UMAP embeddings stashed in the cds object?
Nevermind, I figured it out! It's at cds@int_colData$reducedDims$UMAP On Wednesday, January 31,
Jan 31
Yan Liu
12/28/23
plot_genes_in_pseudotime
Hello everyone, I was trying to do gene expression in pseudotime. Below is my code.
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plot_genes_in_pseudotime
Hello everyone, I was trying to do gene expression in pseudotime. Below is my code.
12/28/23
Kin Sing Lee
, …
Candice Chen
4
12/8/23
there is no package called monocle
Hi, I have also run into the same issue, it took me one day to figure out. So there is actually
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there is no package called monocle
Hi, I have also run into the same issue, it took me one day to figure out. So there is actually
12/8/23
Leticia Rojas
12/5/23
fit_model output fit_coefs table: 'estimate' correct interpretation
Hello everyone, I would like to get the differential expression genes between two conditions ( Old vs
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fit_model output fit_coefs table: 'estimate' correct interpretation
Hello everyone, I would like to get the differential expression genes between two conditions ( Old vs
12/5/23
Cheyenne de Vriend
10/20/23
Error regarding the plot_genes_by function
Hi, Recently I've started working with Monocle3 which I really enjoyed! However, at this point I
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Error regarding the plot_genes_by function
Hi, Recently I've started working with Monocle3 which I really enjoyed! However, at this point I
10/20/23
Gil Stelzer
10/9/23
Which genes govern the decisions at each branchpoint
The tutorial section entitled "Finding genes that change as a function of pseudotime" helps
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Which genes govern the decisions at each branchpoint
The tutorial section entitled "Finding genes that change as a function of pseudotime" helps
10/9/23
Raghumoy Ghosh
8/25/23
Converting CDS to seurat Object
Hi, I am trying to convert a monocle CDS object into a Seurat object. The only function I could find
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Converting CDS to seurat Object
Hi, I am trying to convert a monocle CDS object into a Seurat object. The only function I could find
8/25/23
Kate Laycock
8/13/23
Error message with find_gene_modules
Hello, I am having problems with the find_gene_modules function and would be very grateful for any
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Error message with find_gene_modules
Hello, I am having problems with the find_gene_modules function and would be very grateful for any
8/13/23
Agnes Forsthuber
,
Jun-Hoe Lee
3
8/2/23
smartseq2 RPKM data
That worked, thanks! However I still wonder whether RMPK data is correct to be used with Monocle3 as
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smartseq2 RPKM data
That worked, thanks! However I still wonder whether RMPK data is correct to be used with Monocle3 as
8/2/23
ankit arora
,
Jun-Hoe Lee
3
7/31/23
OrderCells in monocle2
HI Ankit, Please click "reply to group'" next time instead of "to author".
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OrderCells in monocle2
HI Ankit, Please click "reply to group'" next time instead of "to author".
7/31/23
li yue
, …
Matias Andina
5
7/28/23
Error in leidenbase::leiden_find_partition(graph_result[["g"]], partition_type = partition_type, : REAL() can only be applied to a 'numeric', not a 'NULL'
The default method seems problematic, see https://github.com/sib-swiss/single-cell-training/issues/48
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Error in leidenbase::leiden_find_partition(graph_result[["g"]], partition_type = partition_type, : REAL() can only be applied to a 'numeric', not a 'NULL'
The default method seems problematic, see https://github.com/sib-swiss/single-cell-training/issues/48
7/28/23
Vijay Sai
6/29/23
error installing. in r version 4.3.1
Hi, I am trying to install monocle3 in my r and i get the following error. Is there a way to fix?
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error installing. in r version 4.3.1
Hi, I am trying to install monocle3 in my r and i get the following error. Is there a way to fix?
6/29/23
Noé
,
Jun-Hoe Lee
2
6/28/23
Different results when using violin plots and dot plots
Hi, I'm not an expert, but a cursory look through your code and post a few things come to mind: 1
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Different results when using violin plots and dot plots
Hi, I'm not an expert, but a cursory look through your code and post a few things come to mind: 1
6/28/23
Dongeun Heo
,
Jun-Hoe Lee
2
6/22/23
Error: 'clusterCall' is not an exported object from 'namespace:BiocGenerics'
I'm also having the same issue. Did you manage to resolve this? On Sunday, March 27, 2022 at 12:
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Error: 'clusterCall' is not an exported object from 'namespace:BiocGenerics'
I'm also having the same issue. Did you manage to resolve this? On Sunday, March 27, 2022 at 12:
6/22/23
Cherilyn Uhm
6/20/23
Gene Metadata for Importing Data from Already Annotated File in 10x Loupe Browser
Hi, so I am having trouble figuring out how to import my data into R for Monocle 3 analysis. To
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Gene Metadata for Importing Data from Already Annotated File in 10x Loupe Browser
Hi, so I am having trouble figuring out how to import my data into R for Monocle 3 analysis. To
6/20/23
João Gabriel Nascimento Moraes
,
Uday Rangaswamy
2
6/9/23
Error installing monocle3 with conda on HPCC
I know I'm super late but anyways just make sure you have the right version of R installed as
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Error installing monocle3 with conda on HPCC
I know I'm super late but anyways just make sure you have the right version of R installed as
6/9/23
Uday Rangaswamy
5/24/23
Error in rbind(deparse.level, ...) : numbers of columns of arguments do not match
Hi! I'm having the following issue when I run the following : > cds_combined <- combine_cds
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Error in rbind(deparse.level, ...) : numbers of columns of arguments do not match
Hi! I'm having the following issue when I run the following : > cds_combined <- combine_cds
5/24/23
