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Konsta Kukkonen
Jan 4
Giggle index building fails silently / How to test if index is complete?
Hello! I have made custom data set of the UniBind TF binding sites from prostate samples (120
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Giggle index building fails silently / How to test if index is complete?
Hello! I have made custom data set of the UniBind TF binding sites from prostate samples (120
Jan 4
shaoke lou
5/2/23
about cistrome example
Hello, Thanks for your great work developing Giggle score! Recently, we are using Giggle to do some
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about cistrome example
Hello, Thanks for your great work developing Giggle score! Recently, we are using Giggle to do some
5/2/23
zhang xiuxiu
3/25/23
How to calculate the combo score(GIGGLE score)?
Hi Ryan, I am new here.There days I also use the giggle for my work and I am really confused about
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How to calculate the combo score(GIGGLE score)?
Hi Ryan, I am new here.There days I also use the giggle for my work and I am really confused about
3/25/23
tesa.s...@gmail.com
, …
juegaonl...@gmail.com
4
6/24/21
index error with a specific file (roadmap data)
The previous solution did not work for me, I am using CentOS. Instead, I had to modify the file: /etc
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index error with a specific file (roadmap data)
The previous solution did not work for me, I am using CentOS. Instead, I had to modify the file: /etc
6/24/21
June Tan
,
Ryan Layer
2
4/14/21
GIGGLE score = 0 for large single base interval BED file
Sure. Do you have a file you can share? On Wed, Apr 14, 2021 at 3:40 PM June Tan <ytianmcw@gmail.
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GIGGLE score = 0 for large single base interval BED file
Sure. Do you have a file you can share? On Wed, Apr 14, 2021 at 3:40 PM June Tan <ytianmcw@gmail.
4/14/21
Sita Zhou
,
周瑶
3
8/14/19
Q&A
giggle index and search using the same file error
Thanks you for your reply! Unexpected region overlaps exsit in my file, I solved this problem after
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Q&A
giggle index and search using the same file error
Thanks you for your reply! Unexpected region overlaps exsit in my file, I solved this problem after
8/14/19
angela...@gmail.com
,
Ryan Layer
8
8/10/19
Q&A
giggle combo score 0
Hi, I could submit an issue for sure, if you help me what it means exactly, and how to submit... Is
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Q&A
giggle combo score 0
Hi, I could submit an issue for sure, if you help me what it means exactly, and how to submit... Is
8/10/19
wes warren
,
Ryan Layer
2
12/19/18
giggle to index scRNAseq
The closest thing that I have tried is was indexing GTEX expression. To retrieve quantitative data
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giggle to index scRNAseq
The closest thing that I have tried is was indexing GTEX expression. To retrieve quantitative data
12/19/18
ocha...@eng.ucsd.edu
,
Ryan Layer
6
11/27/18
Need a mathematical description of the Fisher contingency table.
Can you send over the two bed files? On Nov 26, 2018, at 12:43 PM, ocha...@eng.ucsd.edu wrote:
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Need a mathematical description of the Fisher contingency table.
Can you send over the two bed files? On Nov 26, 2018, at 12:43 PM, ocha...@eng.ucsd.edu wrote:
11/27/18
Salik Syed
,
Ryan Layer
5
10/29/18
Having trouble replicating the exact Rheumatoid Arthritis example
On Sun, Oct 28, 2018 at 8:56 PM Yudong Qiu <q...@me.com> wrote: Hi Ryan, Thanks a lot for the
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Having trouble replicating the exact Rheumatoid Arthritis example
On Sun, Oct 28, 2018 at 8:56 PM Yudong Qiu <q...@me.com> wrote: Hi Ryan, Thanks a lot for the
10/29/18
F. Requena
,
Ryan Layer
4
10/4/18
Error indexing - Segmentation fault (core dumped)
good luck and let me know if you run into any other issues On Thu, Oct 4, 2018 at 9:10 AM F. Requena
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Error indexing - Segmentation fault (core dumped)
good luck and let me know if you run into any other issues On Thu, Oct 4, 2018 at 9:10 AM F. Requena
10/4/18
ocha...@eng.ucsd.edu
,
Ryan Layer
3
10/1/18
Fisher exact test behavior when query tracks are very different
Using Genomic Hyperbrowser as a Monte-carlo based alternative, ran a query track against a 50 small
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Fisher exact test behavior when query tracks are very different
Using Genomic Hyperbrowser as a Monte-carlo based alternative, ran a query track against a 50 small
10/1/18
Tao Wang
,
Ryan Layer
4
7/9/18
How is the odd ratio calculated? what's the background?
I am afraid I cannot offer much advice here. In general, the GIGGLE score is useful for ranking
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How is the odd ratio calculated? what's the background?
I am afraid I cannot offer much advice here. In general, the GIGGLE score is useful for ranking
7/9/18
peveral...@gmail.com
,
Ryan Layer
2
7/6/18
How to create the cell state name file, etc for creating giggle heatmap
$GIGGLE_ROOT/examples/rme/states.txt column names $GIGGLE_ROOT/examples/rme/EDACC_NAME.txt maps names
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How to create the cell state name file, etc for creating giggle heatmap
$GIGGLE_ROOT/examples/rme/states.txt column names $GIGGLE_ROOT/examples/rme/EDACC_NAME.txt maps names
7/6/18
tesa.s...@gmail.com
,
Ryan Layer
3
6/1/18
how to interpret negative combo score?
Thanks very much for the confirmation. It's always good to know that what you think you
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how to interpret negative combo score?
Thanks very much for the confirmation. It's always good to know that what you think you
6/1/18
Hanqin Li
, …
Ryan Layer
4
4/26/18
Website interface
Sorry about that. The server ran out of disk space. Please try again. On Wed, Apr 25, 2018 at 8:01 PM
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Website interface
Sorry about that. The server ran out of disk space. Please try again. On Wed, Apr 25, 2018 at 8:01 PM
4/26/18
Amir Gamliel
,
Ryan Layer
3
4/18/18
Cistrome example
Hello again, I tried again with the instructions on https://github.com/ryanlayer/giggle/blob/master/
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Cistrome example
Hello again, I tried again with the instructions on https://github.com/ryanlayer/giggle/blob/master/
4/18/18
H Chen
2
3/14/18
Index and file are out of sync
Oh, nvm, the "-f" flag to indicate that I'm re-indexing must appear first: giggle index
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Index and file are out of sync
Oh, nvm, the "-f" flag to indicate that I'm re-indexing must appear first: giggle index
3/14/18
Changson Wan
,
Ryan Layer
2
3/12/18
Too many open files error when using giggle to build the index
Try ulimit -Sn 16384 On Mon, Mar 12, 2018 at 9:08 AM, Changson Wan <wcha...@gmail.com> wrote:
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Too many open files error when using giggle to build the index
Try ulimit -Sn 16384 On Mon, Mar 12, 2018 at 9:08 AM, Changson Wan <wcha...@gmail.com> wrote:
3/12/18
Ryan Layer
3/12/18
Re: Too many open files error
Try ulimit -Sn 16384 On Mon, Mar 12, 2018 at 7:54 AM, Changson Wan <wcha...@gmail.com> wrote:
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Re: Too many open files error
Try ulimit -Sn 16384 On Mon, Mar 12, 2018 at 7:54 AM, Changson Wan <wcha...@gmail.com> wrote:
3/12/18
Pankaj Chopra
,
Ryan Layer
5
2/28/18
download and install?
Ryan, Does the web-browser version work ok? I was trying with the default values, and it doesn't
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download and install?
Ryan, Does the web-browser version work ok? I was trying with the default values, and it doesn't
2/28/18