Recent changes to User Manual

User Manual modified by Congting Ye

Congting Ye — Wed, 01 Sep 2021 01:54:15 -0000

User Manual modified by Congting Ye

Congting Ye — Wed, 01 Sep 2021 01:51:54 -0000

--- v60
+++ v61
@@ -200,7 +200,7 @@
 adjust       -  A multiplicate bandwidth adjustment of the 3' ends density plot. This makes it possible to adjust the bandwidth while still using the a bandwidth estimator. For example, adjust = 1/2 means use half of the default bandwidth. Default, adjust = 1/5.
 heights      -  A numeric vector of length=2 to indicate the ratio of each track (isoform track and 3' ends track). Default, heights = c(0.5,0.5).
 legend.position - The position of legends ("none", "left", "right", "bottom", "top", or two-element numeric vector). Default, legend.position = c(0.8,0.8).
-coord.lim    - Two numeric values, specifying the left and right limit of X-axis, e.g. coord.lim = c(1000,2000).
+coord.lim    -  Two numeric values, specifying the left and right limit of X-axis, e.g. coord.lim = c(1000,2000).
 ```

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User Manual modified by Congting Ye

Congting Ye — Wed, 01 Sep 2021 01:51:24 -0000

--- v59
+++ v60
@@ -49,20 +49,20 @@
 > if (!require("tools")) install.packages("tools")
 ~~~

-###### \[2]. Download and unzip our package - 'scDAPA.zip'
-
-After you download and unzip our scDAPA package, you will see a folder named scDAPA, where 3 Shell scripts and and 1 R package ('scDAPAminer_1.0.tar.gz') are located.
+###### \[2]. Download and unzip our package - 'scDAPA.20210901.zip'
+
+After you download and unzip our scDAPA package, you will see a folder named scDAPA, where 3 Shell scripts and and 1 R package ('scDAPAminer_1.1.tar.gz') are located.

 ###### \[3]. Add executable permissions
 ~~~
 $ chmod +x extractReads.sh extractGenes.sh annotate3Ends.sh
 ~~~

-###### \[4]. Install R package 'scDAPAminer_1.0.tar.gz'
-
-You shoule make sure the R environment is installed. After opening the R, change the R's **Working Path** to the path where 'scDAPAminer_1.0.tar.gz' is located (e.g., './scDAPA'). Type the following command in the **Command Window** of R:
-~~~
-> install.packages("scDAPAminer_1.0.tar.gz",repos = NULL, type = "source")
+###### \[4]. Install R package 'scDAPAminer_1.1.tar.gz'
+
+You shoule make sure the R environment is installed. After opening the R, change the R's **Working Path** to the path where 'scDAPAminer_1.1.tar.gz' is located (e.g., './scDAPA'). Type the following command in the **Command Window** of R:
+~~~
+> install.packages("scDAPAminer_1.1.tar.gz",repos = NULL, type = "source")
 ~~~

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@@ -200,6 +200,7 @@
 adjust       -  A multiplicate bandwidth adjustment of the 3' ends density plot. This makes it possible to adjust the bandwidth while still using the a bandwidth estimator. For example, adjust = 1/2 means use half of the default bandwidth. Default, adjust = 1/5.
 heights      -  A numeric vector of length=2 to indicate the ratio of each track (isoform track and 3' ends track). Default, heights = c(0.5,0.5).
 legend.position - The position of legends ("none", "left", "right", "bottom", "top", or two-element numeric vector). Default, legend.position = c(0.8,0.8).
+coord.lim    - Two numeric values, specifying the left and right limit of X-axis, e.g. coord.lim = c(1000,2000).
 ```

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User Manual modified by Congting Ye

Congting Ye — Thu, 22 Apr 2021 08:00:08 -0000

--- v58
+++ v59
@@ -264,6 +264,8 @@
 > # customize simultaneuouly
 > dp + scale_colour_aaas() + labs(colour = "Cell type") + theme(legend.position = c(0.6, 0.9))
 ```
+![Figure 1](https://sourceforge.net/p/scdapa/wiki/User%20Manual/attachment/1.png)
+
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User Manual modified by Congting Ye

Congting Ye — Thu, 22 Apr 2021 07:57:16 -0000

User Manual modified by Congting Ye

Congting Ye — Thu, 22 Apr 2021 07:55:04 -0000

--- v56
+++ v57
@@ -29,7 +29,7 @@

 ---
 ###### \[1]. Install dependencies of scDAPA
-Install softwares: [SAMtools](http://samtools.sourceforge.net/), [bedtools](https://bedtools.readthedocs.io/en/latest/), and [R](https://www.r-project.org/).
+Install softwares: [GNU Awk](https://www.gnu.org/software/gawk/), [SAMtools](http://samtools.sourceforge.net/), [bedtools](https://bedtools.readthedocs.io/en/latest/), and [R](https://www.r-project.org/).
 Install R packages: tools, stringr, rtracklayer, ggplot2, ggbio. If R >=3.5.0. ,
 ~~~
 > if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

User Manual modified by Congting Ye

Congting Ye — Sun, 08 Mar 2020 11:38:56 -0000

--- v55
+++ v56
@@ -18,6 +18,8 @@
 ---

 **scDAPA** is a tool capable of identifying and visualizing dynamic alternative polyadenylation (APA) from scRNA-seq data. 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 this website.
+
+[Ye C, Zhou Q, Wu X, Yu C, Ji G, Saban D. R., Li Q. Q. (2020) scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data. ***Bioinformatics*** 36(4): 1262–1264.](https://academic.oup.com/bioinformatics/article-abstract/36/4/1262/5564118) 

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</yec@xmu.edu.cn>

User Manual modified by Congting Ye

Congting Ye — Mon, 24 Feb 2020 03:47:05 -0000

--- v54
+++ v55
@@ -87,7 +87,7 @@
 ###### Parameters:
 ~~~
 -r|-read   a file of short reads mapping result in bam/sam format.
--c|-cluster    a csv format file of cell clustering result, the first coloumn is cell barcode, and the second coloumn is cluster label.
+-c|-cluster    a csv format file of cell clustering result, the first column is cell barcode, and the second column is cluster label.
 -o|-output a output directory, if not set, files of extracted reads will be stored in current working path.
 ~~~

@@ -277,7 +277,7 @@

 
  
 ##### \[2] Format of cell classification result
-A comma-separated values (CSV) file, the first coloumn is cell barcodes, and the second coloumn is cluster labels. 
+A comma-separated values (CSV) file, the first column is cell barcodes, and the second column is cluster labels. 

 |Column Name | Explanation | 
 |:---------- |:----------|

User Manual modified by Congting Ye

Congting Ye — Tue, 23 Jul 2019 06:42:40 -0000

--- v53
+++ v54
@@ -293,7 +293,7 @@
 ---

 ##### \[1] Output of **annotate3Ends.sh** is a 11 columns tab-separated values file (.anno):
-For "+" strand gene, 3′ ends is stored in the column 'end of reads'; For "-" strand gene, 3′ ends is stored in the column 'start of read'.
+For "+" strand gene, 3′ ends is stored in the column 'end of read'; For "-" strand gene, 3′ ends is stored in the column 'start of read'.

 |Column Name | Explanation | 
 |:---------- |:----------|

User Manual modified by Congting Ye

Congting Ye — Tue, 23 Jul 2019 06:39:13 -0000

--- v52
+++ v53
@@ -208,7 +208,7 @@

 ---

-Steps of using scDAPA to process  data from 10x Genomics:
+Steps of using scDAPA to process  test data from 10x Genomics:

 *   **Preparation  of necessary data**