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Gonzalo Soria Alcaide
Feb 16
Error when using check_markers
Hi all, First of all, I recently found your tool in some Tcell annotation reviews and I loved the
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Error when using check_markers
Hi all, First of all, I recently found your tool in some Tcell annotation reviews and I loved the
Feb 16
Moritz Przybilla
, …
hpl...@gmail.com
5
10/26/23
Train marker-free classifier: Error in .testForValidKeys(x, keys, keytype, fks)
Sorry for the very long delay. I don't see an obvious issue here... you're certain that the
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Train marker-free classifier: Error in .testForValidKeys(x, keys, keytype, fks)
Sorry for the very long delay. I don't see an obvious issue here... you're certain that the
10/26/23
Jinhong Kim
,
hpl...@gmail.com
2
8/3/23
error on check_markers for 'SYMBOL'
Hi Jinhong, sorry for the delay. The cell_id_type refers to the gene type of the cds function, which
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error on check_markers for 'SYMBOL'
Hi Jinhong, sorry for the delay. The cell_id_type refers to the gene type of the cds function, which
8/3/23
Justine Seow
,
hpl...@gmail.com
2
5/4/23
Garnett on VISIUM
Hi Justine, I haven't tried to run Garnett on Visium data. On an engineering level you should be
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Garnett on VISIUM
Hi Justine, I haven't tried to run Garnett on Visium data. On an engineering level you should be
5/4/23
Piyal saha
,
hpl...@gmail.com
2
12/3/22
Training classifier
Hello, You can do either, either train on published data (and in that case I would recommend using
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Training classifier
Hello, You can do either, either train on published data (and in that case I would recommend using
12/3/22
Jordi Camps
,
hpl...@gmail.com
2
9/20/20
Testing different tissues with a training dataset
Hi Jordi, It's tough to give you exact recommendations without knowing a bit more context, but a
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Testing different tissues with a training dataset
Hi Jordi, It's tough to give you exact recommendations without knowing a bit more context, but a
9/20/20
chris briggs
,
Hannah A Pliner
2
7/24/20
Q&A
interactive disconnects after PBMC data loaded
Hi Chris, From what I see looking at the log files, it appears that the instance is running out of
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Q&A
interactive disconnects after PBMC data loaded
Hi Chris, From what I see looking at the log files, it appears that the instance is running out of
7/24/20
James Hong
,
Hannah Pliner
4
3/17/20
Is it possible to use the mouse CNS classifier as a starting point for human or rat CNS tissue?
Hi James, If the gene names are compatible (and mark the same thing in rat as in mouse) then I don
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Is it possible to use the mouse CNS classifier as a starting point for human or rat CNS tissue?
Hi James, If the gene names are compatible (and mark the same thing in rat as in mouse) then I don
3/17/20
James Hong
,
Hannah Pliner
3
3/9/20
two species in sample with garnett
Thank you! It's already set up like that, so this is perfect. Will test it. James Sent from my
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two species in sample with garnett
Thank you! It's already set up like that, so this is perfect. Will test it. James Sent from my
3/9/20
payal banerjee
,
Robert Alpin
6
3/4/20
Organism other than Human or Mouse
Thanks! Yes I am going over their tutorials. I just saw a new feature "Train a marker-free
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Organism other than Human or Mouse
Thanks! Yes I am going over their tutorials. I just saw a new feature "Train a marker-free
3/4/20
Eric Kernfeld
,
Hannah Pliner
3
2/19/20
Automatic marker file creation?
Hi Eric, Heads up that I have just pushed the new marker-free version of garnett (in alpha and only
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Automatic marker file creation?
Hi Eric, Heads up that I have just pushed the new marker-free version of garnett (in alpha and only
2/19/20
biomiha
,
Hannah Pliner
3
2/19/20
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘colData’ for signature ‘"CellDataSet"’
Hi Hannah, Yes, you're right. I was using the wrong combination of monocle3 and garnett. This now
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Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘colData’ for signature ‘"CellDataSet"’
Hi Hannah, Yes, you're right. I was using the wrong combination of monocle3 and garnett. This now
2/19/20
S Hui
,
Hannah Pliner
2
11/12/19
Q&A
Error in RANN::nn2
That error looks like there aren't enough cells to compute a nearest neighbors tree. Are you
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Q&A
Error in RANN::nn2
That error looks like there aren't enough cells to compute a nearest neighbors tree. Are you
11/12/19
S Hui
, …
Robert Alpin
3
10/25/19
Q&A
Many cell definitions dropped
I was also confused about the train/classify aspect of Garnett. It feels to me like the tutorial
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Q&A
Many cell definitions dropped
I was also confused about the train/classify aspect of Garnett. It feels to me like the tutorial
10/25/19
Eric
, …
Robert Alpin
5
10/7/19
"High overlap" despite mutually exclusive conditions?
Running it with the pre-downloaded data set and those terms behaves as expected: I'm not sure why
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"High overlap" despite mutually exclusive conditions?
Running it with the pre-downloaded data set and those terms behaves as expected: I'm not sure why
10/7/19
Robert Alpin
,
Hannah Pliner
2
10/7/19
A handfull of questions
Hello, I'll respond in order: Usually a handful of 'good' markers is superior to a lot of
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A handfull of questions
Hello, I'll respond in order: Usually a handful of 'good' markers is superior to a lot of
10/7/19
Xin Yi
,
Hannah Pliner
3
9/11/19
Got an error when run "Check the classifier" part
Hi Hannah, Thanks for your remind. Actually,yeah. I used a file editor software and found out that
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Got an error when run "Check the classifier" part
Hi Hannah, Thanks for your remind. Actually,yeah. I used a file editor software and found out that
9/11/19
Jin Ye
,
Hannah Pliner
2
9/11/19
marker file have 30 clusters
Hi Jin, I'm not sure why that would happen. What does your "check_markers" plot look
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marker file have 30 clusters
Hi Jin, I'm not sure why that would happen. What does your "check_markers" plot look
9/11/19
Eric
,
Hannah A Pliner
3
8/16/19
How to interpret marker_score N/A
Ahhh...I get it. Makes sense. Thanks!
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How to interpret marker_score N/A
Ahhh...I get it. Makes sense. Thanks!
8/16/19
david.sanin
, …
Hannah A Pliner
5
7/31/19
Ambiguous dimensionality error while training classifier
That fixed the problem. Now it runs smoothly to the end! Thanks for your help! David On Tuesday, 30
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Ambiguous dimensionality error while training classifier
That fixed the problem. Now it runs smoothly to the end! Thanks for your help! David On Tuesday, 30
7/31/19
Dan Schnell
,
Hannah Pliner
3
7/30/19
Not enough training samples for any cell types at root of cell type hierarchy!
Thanks very much for your reply Hannah. I will update the installation of monocle3. Also, I saw some
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Not enough training samples for any cell types at root of cell type hierarchy!
Thanks very much for your reply Hannah. I will update the installation of monocle3. Also, I saw some
7/30/19
Connor Finkbeiner
,
Hannah Pliner
2
7/26/19
Marker file error "arker file error. Illegal character"
I think this might be caused by the backwards slash in your file path. Can you try running it again
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Marker file error "arker file error. Illegal character"
I think this might be caused by the backwards slash in your file path. Can you try running it again
7/26/19
Jessie Huang
,
Hannah A Pliner
4
7/16/19
Q&A
db = 'none' is not working
I believe this issue is solved in the most recent version of the monocle3 branch and I will push a
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Q&A
db = 'none' is not working
I believe this issue is solved in the most recent version of the monocle3 branch and I will push a
7/16/19
Noah Simons
,
Hannah A Pliner
3
6/10/19
Q&A
train classifier on bulk RNA-seq dataset
Hi Hannah, Ok, that's even better then! Thanks very much! Noah On Monday, June 10, 2019 at 1:12:
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Q&A
train classifier on bulk RNA-seq dataset
Hi Hannah, Ok, that's even better then! Thanks very much! Noah On Monday, June 10, 2019 at 1:12:
6/10/19
An Lau
,
Hannah A Pliner
4
6/9/19
Q&A
problem with classify_cells results
Hi Hannah, Thank you for the clarification. I will try it. An Hannah A Pliner <hpl...@uw.edu>
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Q&A
problem with classify_cells results
Hi Hannah, Thank you for the clarification. I will try it. An Hannah A Pliner <hpl...@uw.edu>
6/9/19
alex.ta...@gmail.com
, …
Hannah Pliner
4
5/7/19
Classification weighted by number of marker genes?
Thanks Hannah. I'm finding Garnett very valuable and I really appreciate your help with my
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Classification weighted by number of marker genes?
Thanks Hannah. I'm finding Garnett very valuable and I really appreciate your help with my
5/7/19
tomj...@gmail.com
,
Hannah A Pliner
2
5/1/19
problem with marker file creation
Hi Tom, Looks to me like you're inputing the marker info into the command line. You need to put
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problem with marker file creation
Hi Tom, Looks to me like you're inputing the marker info into the command line. You need to put
5/1/19
thao....@gmail.com
,
Hannah A Pliner
2
4/16/19
Problem with training my dataset - only few cells got trained into limited cell types
Generally when cells aren't chosen for the training set it indicates that the markers aren't
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Problem with training my dataset - only few cells got trained into limited cell types
Generally when cells aren't chosen for the training set it indicates that the markers aren't
4/16/19
Isaiah
, …
Hannah A Pliner
13
3/16/19
marker file error
Yup, that'll do it. Size factors are a scaling factor based on the geometric mean of the column
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marker file error
Yup, that'll do it. Size factors are a scaling factor based on the geometric mean of the column
3/16/19
RS
, …
Hannah Pliner
4
3/4/19
How to obtain tSNE plots
Either of the plotting methods you mention will work. You can plot them using plot_cell_clusters in
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How to obtain tSNE plots
Either of the plotting methods you mention will work. You can plot them using plot_cell_clusters in
3/4/19