Recent changes to User Manual

User Manual modified by Congting Ye

Congting Ye — Wed, 01 Sep 2021 02:00:07 -0000

--- v10
+++ v11
@@ -28,6 +28,8 @@

 If you have any question or comment, please contact with Dr. Congting Ye(<yec@xmu.edu.cn>). You can also report a bug as a Ticket request, or start a topic session in the Discussion webpage of the QuantifyPoly(A) website.

+[Ye C, Zhao D, Ye W, Wu X, Ji G, Li Q. Q., Lin J (2021) QuantifyPoly(A): reshaping alternative polyadenylation landscapes of eukaryotes with weighted density peak clustering. ***Briefings in Bioinformatics***  doi: 10.1093/bib/bbab268](https://doi.org/10.1093/bib/bbab268) 
+
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@@ -321,7 +323,7 @@
 anno - A Granges object of gene model info. It could be generated using the function 'import' of R package 'rtracklayer', e.g. gtf = import('./Mus_musculus.GRCm38.84.gtf')
 gene.id - A string indicating the gene to be visualized, e.g. gene.id = 'ENSMUSG00000073490'.
 sample.names - A character vector specifying the samples to be visualized. If not defined, all samples will display.
-coord.lim - Two numeric values, specifying the left and right limit of xaxis.
+coord.lim - Two numeric values, specifying the left and right limit of X-axis.
 ~~~

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</yec@xmu.edu.cn>

User Manual modified by Congting Ye

Congting Ye — Wed, 16 Jun 2021 04:41:29 -0000

--- v9
+++ v10
@@ -92,16 +92,16 @@
 > if (!require("ggbio")) BiocInstaller::biocLite("ggbio")
 ~~~

-###### \[2]. Download our package - 'QuantifyPolyA_0.2.0.tar.gz'
+###### \[2]. Download our package - 'QuantifyPolyA_0.X.0.tar.gz'

 Go to the webpage of the QuantifyPoly(A), click the 'Files' tab to download the latest version of QuantifyPoly(A) and related test dataset.

-###### \[3]. Install R package 'QuantifyPolyA_0.2.0.tar.gz'
-
-You should make sure the R environment is installed. After opening the R, change the R's **Working Path** to the path where 'QuantifyPolyA_0.2.0.tar.gz' is located (*e.g.*, './Downloads'). Type the following command in the **Command Window** of R:
-
-~~~
-> install.packages("QuantifyPolyA_0.2.0.tar.gz",repos = NULL, type = "source")
+###### \[3]. Install R package 'QuantifyPolyA_0.X.0.tar.gz'
+
+You should make sure the R environment is installed. After opening the R, change the R's **Working Path** to the path where 'QuantifyPolyA_0.X.0.tar.gz' is located (*e.g.*, './Downloads'). Type the following command in the **Command Window** of R:
+
+~~~
+> install.packages("QuantifyPolyA_0.X.0.tar.gz",repos = NULL, type = "source")
 ~~~

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User Manual modified by Congting Ye

Congting Ye — Mon, 22 Mar 2021 09:52:54 -0000

--- v8
+++ v9
@@ -510,7 +510,7 @@
 > anno = import('Homo_sapiens.GRCh38.101.gtf')

 > # Get poly(A) profiles of specific genes.
-> gene_id = 'ENSG00000100731'
+> gene_id = 'ENSG00000164091'
 > dp = Visualize.PolyA(QpolyA,anno,gene_id,coord.lim=c(52254310,52255210))

 > # Customize the plot.

User Manual modified by Congting Ye

Congting Ye — Wed, 17 Mar 2021 04:57:34 -0000

User Manual modified by Congting Ye

Congting Ye — Wed, 17 Mar 2021 04:54:30 -0000

--- v6
+++ v7
@@ -92,16 +92,16 @@
 > if (!require("ggbio")) BiocInstaller::biocLite("ggbio")
 ~~~

-###### \[2]. Download our package - 'QuantifyPolyA_0.1.0.tar.gz'
+###### \[2]. Download our package - 'QuantifyPolyA_0.2.0.tar.gz'

 Go to the webpage of the QuantifyPoly(A), click the 'Files' tab to download the latest version of QuantifyPoly(A) and related test dataset.

-###### \[3]. Install R package 'QuantifyPolyA_0.1.0.tar.gz'
-
-You should make sure the R environment is installed. After opening the R, change the R's **Working Path** to the path where 'QuantifyPolyA_0.1.0.tar.gz' is located (*e.g.*, './Downloads'). Type the following command in the **Command Window** of R:
-
-~~~
-> install.packages("QuantifyPolyA_0.1.0.tar.gz",repos = NULL, type = "source")
+###### \[3]. Install R package 'QuantifyPolyA_0.2.0.tar.gz'
+
+You should make sure the R environment is installed. After opening the R, change the R's **Working Path** to the path where 'QuantifyPolyA_0.2.0.tar.gz' is located (*e.g.*, './Downloads'). Type the following command in the **Command Window** of R:
+
+~~~
+> install.packages("QuantifyPolyA_0.2.0.tar.gz",repos = NULL, type = "source")
 ~~~

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@@ -511,7 +511,7 @@

 > # Get poly(A) profiles of specific genes.
 > gene_id = 'ENSG00000100731'
-> dp = Visualize.PolyA(QpolyA,anno,gene_id)
+> dp = Visualize.PolyA(QpolyA,anno,gene_id,coord.lim=c(52254310,52255210))

 > # Customize the plot.
 > library(ggsci)

User Manual modified by Congting Ye

Congting Ye — Thu, 07 Jan 2021 09:02:40 -0000

--- v5
+++ v6
@@ -113,7 +113,7 @@

 There are 6 major steps of running QuantifyPoly(A): (**a**) input preparing; (**b**) internal priming artifact removing; (**c**) poly(A) site clustering; (**d**) feature annotation; (**e**) APA dynamics detection; (**f**) APA visualization (see Figure 1).

- ![Figure 1](https://sourceforge.net/p/quantifypoly-a/wiki/_discuss/thread/44f456028a/d51b/attachment/image-20201210204028033.png)
+ ![Figure 1](https://sourceforge.net/p/quantifypoly-a/wiki/User%20Manual/attachment/Figure1.png)

 Figure 1. The schematic diagram of QuantifyPoly(A). 

@@ -411,7 +411,7 @@
 > dp + scale_color_aaas() + scale_fill_aaas()
 ```

-![image-20201211135011930](C:\Users\yec\AppData\Roaming\Typora\typora-user-images\image-20201211135011930.png)
+![Figure 2](https://sourceforge.net/p/quantifypoly-a/wiki/User%20Manual/attachment/Figure2.png)

 Figure 2. Illustration of a gene *CIPK9* showing dynamic APA profiles between wild type (*wt*) and double mutants (*fy3oxt6*) samples.

@@ -434,7 +434,7 @@
 > res$PCA.Plot
 ```

-![image-20201211140132526](C:\Users\yec\AppData\Roaming\Typora\typora-user-images\image-20201211140132526.png)
+![Figure 3](https://sourceforge.net/p/quantifypoly-a/wiki/User%20Manual/attachment/Figure3.png)

  Figure 3. The PCA plot based on the PAC matrix.

@@ -518,7 +518,7 @@
 > dp + scale_color_aaas() + scale_fill_aaas()
 ```

-![image-20201211142650547](C:\Users\yec\AppData\Roaming\Typora\typora-user-images\image-20201211142650547.png)
+![Figure 4](https://sourceforge.net/p/quantifypoly-a/wiki/User%20Manual/attachment/Figure4.png)

 Figure 4. Illustration of a gene *PCNX1* showing dynamic APA profiles between brain and UHR samples.

@@ -541,7 +541,7 @@
 > res$PCA.Plot
 ```

-![image-20201211143205533](C:\Users\yec\AppData\Roaming\Typora\typora-user-images\image-20201211143205533.png)
+![Figure 5](https://sourceforge.net/p/quantifypoly-a/wiki/User%20Manual/attachment/Figure5.png)

  Figure 5. The PCA plot based on the PAC matrix.

User Manual modified by Congting Ye

Congting Ye — Thu, 07 Jan 2021 08:56:42 -0000

User Manual modified by Congting Ye

Congting Ye — Thu, 07 Jan 2021 08:53:25 -0000

--- v3
+++ v4
@@ -113,7 +113,7 @@

 There are 6 major steps of running QuantifyPoly(A): (**a**) input preparing; (**b**) internal priming artifact removing; (**c**) poly(A) site clustering; (**d**) feature annotation; (**e**) APA dynamics detection; (**f**) APA visualization (see Figure 1).

- ![Figure 1](https://sourceforge.net/p/quantifypoly-a/wiki/User%20Manual/#d51b)
+ ![Figure 1](https://sourceforge.net/p/quantifypoly-a/wiki/_discuss/thread/44f456028a/d51b/attachment/image-20201210204028033.png)

 Figure 1. The schematic diagram of QuantifyPoly(A).

User Manual modified by Congting Ye

Congting Ye — Thu, 07 Jan 2021 08:52:07 -0000

--- v2
+++ v3
@@ -113,7 +113,7 @@

 There are 6 major steps of running QuantifyPoly(A): (**a**) input preparing; (**b**) internal priming artifact removing; (**c**) poly(A) site clustering; (**d**) feature annotation; (**e**) APA dynamics detection; (**f**) APA visualization (see Figure 1).

-![image-20201210204028033](C:\Users\yec\AppData\Roaming\Typora\typora-user-images\image-20201210204028033.png) ![](https://)
+ ![Figure 1](https://sourceforge.net/p/quantifypoly-a/wiki/User%20Manual/#d51b)

 Figure 1. The schematic diagram of QuantifyPoly(A).

Discussion for User Manual page

Congting Ye — Thu, 07 Jan 2021 08:50:46 -0000

schematic diagram