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Gonzalo Olivares
12/23/24
Dapars2 output file
Dear all, I run Dapars 2 on 48 Drosophila samples and I got an output file which contain info that I
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Dapars2 output file
Dear all, I run Dapars 2 on 48 Drosophila samples and I got an output file which contain info that I
12/23/24
熊鸣
,
Lometry Sun
2
11/6/23
Help on using scDaPars
I had the same issue recently, I have searched online but no method works. Have you solve this
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Help on using scDaPars
I had the same issue recently, I have searched online but no method works. Have you solve this
11/6/23
oliver...@gmail.com
, …
Chen Jin
5
2/22/23
Q&A
Sudden IndexError
Hello, I have encountered the same problem, but I still can't solve it after trying various
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Q&A
Sudden IndexError
Hello, I have encountered the same problem, but I still can't solve it after trying various
2/22/23
lu lu
1/26/23
how to get reference genome annotation and refseq_IDmapping.txt from gencode? or generate by myself?
Hi Zheng, My RNA-seq data is aligned to Gencode using STAR, as you mentioned, the reference genome
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how to get reference genome annotation and refseq_IDmapping.txt from gencode? or generate by myself?
Hi Zheng, My RNA-seq data is aligned to Gencode using STAR, as you mentioned, the reference genome
1/26/23
haife...@gmail.com
,
Kathryn Jackson-Jones
2
11/23/22
Q&A
How to explain the result output file
Hello, I have the same question, basically how to understand the columns in the output folder.
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Q&A
How to explain the result output file
Hello, I have the same question, basically how to understand the columns in the output folder.
11/23/22
liu...@gmail.com
, …
Kathryn Jackson-Jones
3
11/23/22
Q&A
How to interpret the outputs?
Hello, I am wondering the same question and wondering if anyone has found a description for what each
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Q&A
How to interpret the outputs?
Hello, I am wondering the same question and wondering if anyone has found a description for what each
11/23/22
Renhua Song
, …
Zheng Xia
3
10/15/22
Q&A
rpy2 problem
We removed rpy2 dependence now. Thanks, Zheng On Friday, June 25, 2021 at 9:48:56 AM UTC-7 Srinivasan
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Q&A
rpy2 problem
We removed rpy2 dependence now. Thanks, Zheng On Friday, June 25, 2021 at 9:48:56 AM UTC-7 Srinivasan
10/15/22
Sean Mark
11/16/21
Dealing with replicates across different treatment groups?
Hello, I am trying to understand how DaPARS2 deals with biological replicates and compares two
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Dealing with replicates across different treatment groups?
Hello, I am trying to understand how DaPARS2 deals with biological replicates and compares two
11/16/21
Farica Zhuang
, …
Farica Zhuang
5
9/22/21
Running DaPars with sample files without leading "chr" and Ensembl gene model
Yes good idea, thank you! On Saturday, August 28, 2021 at 12:17:11 AM UTC-4 tians...@gmail.com wrote:
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Running DaPars with sample files without leading "chr" and Ensembl gene model
Yes good idea, thank you! On Saturday, August 28, 2021 at 12:17:11 AM UTC-4 tians...@gmail.com wrote:
9/22/21
bioapa
2
5/21/21
scDapars & DaPars
在2021年5月21日星期五 UTC+8 下午4:21:02<bioapa> 写道： How to convert the running result of DaPars2 into
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scDapars & DaPars
在2021年5月21日星期五 UTC+8 下午4:21:02<bioapa> 写道： How to convert the running result of DaPars2 into
5/21/21
fitzsimmonscm
5/8/21
Pushing DaPars to Bioconda for APAeval
Hi Zheng, As part of the RNA Society meeting this year, the community is organizing a hackathon to
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Pushing DaPars to Bioconda for APAeval
Hi Zheng, As part of the RNA Society meeting this year, the community is organizing a hackathon to
5/8/21
Cheng Zou
4/13/20
Q&A
ERROR: numpy requires Python '>=3.5' but the running Python is 2.7.16
Hi, When I try to analysis APA by DaPars (not DaPars2), I got the problem like"ERROR: numpy
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Q&A
ERROR: numpy requires Python '>=3.5' but the running Python is 2.7.16
Hi, When I try to analysis APA by DaPars (not DaPars2), I got the problem like"ERROR: numpy
4/13/20
yue li
,
pinjo...@gmail.com
2
11/5/19
Q&A
rpy2 is no longer supporting Python2 and there is no older version of rpy2, so how to setup rpy2
Hi Yue Li, Try install rpy2 with conda. There are several previous versions of rpy2 and the one v2.
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Q&A
rpy2 is no longer supporting Python2 and there is no older version of rpy2, so how to setup rpy2
Hi Yue Li, Try install rpy2 with conda. There are several previous versions of rpy2 and the one v2.
11/5/19
cheungx...@gmail.com
, …
habo...@uci.edu
5
7/10/19
Q&A
ValueError: invalid literal for int() with base 10: '1.00995e+06'
Thanks for the response, I had downloaded from github version 0.9.1 which I thought was the newest
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Q&A
ValueError: invalid literal for int() with base 10: '1.00995e+06'
Thanks for the response, I had downloaded from github version 0.9.1 which I thought was the newest
7/10/19
menon...@gmail.com
,
lybi...@gmail.com
2
10/31/18
Q&A
LookupError: 'show' not found
On Wednesday, October 11, 2017 at 3:05:16 AM UTC+8, menon...@gmail.com wrote: > Hello, > I have
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Q&A
LookupError: 'show' not found
On Wednesday, October 11, 2017 at 3:05:16 AM UTC+8, menon...@gmail.com wrote: > Hello, > I have
10/31/18
Zhixia Xiao
, …
puttyx
11
8/23/18
Q&A
How DaPars deal with multiple replicates?
Hi puttyx, The group information was not used when estimating P* or isoform expression, after P* and
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Q&A
How DaPars deal with multiple replicates?
Hi puttyx, The group information was not used when estimating P* or isoform expression, after P* and
8/23/18
khand...@gmail.com
7/17/18
Q&A
Non-uniformity correction
Hi, In your publication where you present DaPars (doi:10.1038/ncomms6274), you mention a process for
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Q&A
Non-uniformity correction
Hi, In your publication where you present DaPars (doi:10.1038/ncomms6274), you mention a process for
7/17/18
cao...@gmail.com
, …
exu123
4
6/19/18
Q&A
NA in the Dapars results
I have a related question about the DaPars results, why some genes appear multiple times with
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Q&A
NA in the Dapars results
I have a related question about the DaPars results, why some genes appear multiple times with
6/19/18
jcrow...@gmail.com
, …
jto...@rupskee.com
4
5/8/18
Q&A
rpy2 import problems
On Tuesday, June 9, 2015 at 4:41:35 AM UTC-4, jcrow...@gmail.com wrote: > I have figured out the
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Q&A
rpy2 import problems
On Tuesday, June 9, 2015 at 4:41:35 AM UTC-4, jcrow...@gmail.com wrote: > I have figured out the
5/8/18
swat...@gmail.com
4/12/18
Q&A
Do the normal samples need to be "matched" normal for DaPars1?
I have normal samples from GTeX and tumor samples from TCGA aligned identically. If I want to compare
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Q&A
Do the normal samples need to be "matched" normal for DaPars1?
I have normal samples from GTeX and tumor samples from TCGA aligned identically. If I want to compare
4/12/18
elva.x...@gmail.com
1/24/18
Q&A
dapars with multiple wig files in each group failed
hi, I tried to run DaPars with 200 wig files in each group,but it always failed,is there some way to
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Q&A
dapars with multiple wig files in each group failed
hi, I tried to run DaPars with 200 wig files in each group,but it always failed,is there some way to
1/24/18
zxue....@gmail.com
12/11/17
Q&A
Does DaPars consider each transcript independently?
I am looking through the DaPars code, and it seems to me that DaPars consider the 3' UTR coverage
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Q&A
Does DaPars consider each transcript independently?
I am looking through the DaPars code, and it seems to me that DaPars consider the 3' UTR coverage
12/11/17
Xia, Zheng
,
zxue....@gmail.com
2
12/11/17
Re: Looking fo help for the usage of DaPars
Hi Zheng, I have exactly the same question, my output look like Gene fit_value Predicted_Proximal_APA
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Re: Looking fo help for the usage of DaPars
Hi Zheng, I have exactly the same question, my output look like Gene fit_value Predicted_Proximal_APA
12/11/17
menon...@gmail.com
,
Xin....@bcm.edu
2
11/1/17
Q&A
value error
please check your wiggle file, it has to be the format of bedgraph. chr19 49302000 49302300 -1.0
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Q&A
value error
please check your wiggle file, it has to be the format of bedgraph. chr19 49302000 49302300 -1.0
11/1/17
Zheng Xia
7/2/17
Re: DaPars Extract Anno
Including the last exon along with 3'UTR helps identify the density change along the 3'UTR.
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Re: DaPars Extract Anno
Including the last exon along with 3'UTR helps identify the density change along the 3'UTR.
7/2/17
Tsviya Olender
,
Adam Malinowski
2
5/9/17
UnboundLocalError: local variable 'chrom_name' referenced before assignment
Why this dont work? http://wypozyczalnia-wroclaw.pl ??? W dniu środa, 30 listopada 2016 11:45:09 UTC+
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UnboundLocalError: local variable 'chrom_name' referenced before assignment
Why this dont work? http://wypozyczalnia-wroclaw.pl ??? W dniu środa, 30 listopada 2016 11:45:09 UTC+
5/9/17
yolanda...@gmail.com
5/2/17
Q&A
false positive
Dear Zheng Xia, I'm trying to use DaPars for detecting APA site usage of my RNA-Seq data. I
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Q&A
false positive
Dear Zheng Xia, I'm trying to use DaPars for detecting APA site usage of my RNA-Seq data. I
5/2/17
johnath...@gmail.com
4/6/17
Q&A
DaPars Results from Nature Communications Paper
Hi Xia, Do you have the DaPars generated results file (similar to the one in your github) used in the
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Q&A
DaPars Results from Nature Communications Paper
Hi Xia, Do you have the DaPars generated results file (similar to the one in your github) used in the
4/6/17
Zheng Xia
11/28/16
Re: Missing parentheses in DaPar
Hi Tsviya, DaPars is developed in Python2.7. So please use python2.7 instead of python3. Thanks,
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Re: Missing parentheses in DaPar
Hi Tsviya, DaPars is developed in Python2.7. So please use python2.7 instead of python3. Thanks,
11/28/16
Wei Tang
9/6/16
Q&A
DaPars processed TCGA data available?
Hi Xia, I read your Nat Communication Paper about processing TCGA data and reported numerous APA
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Q&A
DaPars processed TCGA data available?
Hi Xia, I read your Nat Communication Paper about processing TCGA data and reported numerous APA
9/6/16
