Recent changes to Home

Home modified by Kleber Padovani de Souza

Kleber Padovani de Souza — Wed, 01 Aug 2018 17:59:26 -0000

--- v19
+++ v20
@@ -21,4 +21,4 @@
 * quality: HTML files corresponding to quality reports of each read sample file obtained by FastQC tool (README.txt file contains a brief explanation about each report)
 * SoilSamples.csv: a CSV file containing chemical metadata about each soil sample

-If you have any trouble with these files, contact us by [someemail@itv.org](mailto:someemail@itv.org).
+If you have any trouble with these files, contact us by [guilherme.oliveira@itv.org](mailto:guilherme.oliveira@itv.org).

Home modified by Kleber Padovani de Souza

Kleber Padovani de Souza — Wed, 01 Aug 2018 17:52:56 -0000

--- v18
+++ v19
@@ -1,5 +1,4 @@
-This project contains supplementary files used to produce the data presented in the paper entitled [A metagenomic survey of soil microbial communities along a
-rehabilitation chronosequence after iron ore mining](https://www.nature.com/sdata/).
+This project contains supplementary files used to produce the data presented in the paper entitled [A metagenomic survey of soil microbial communities along a rehabilitation chronosequence after iron ore mining](https://www.nature.com/sdata/).

 Click [here](https://sourceforge.net/projects/corumba/files/) to download files. Other input files can be downloaded at NCBI website. Paired-end reads and contig files can be downloaded [here](https://www.ncbi.nlm.nih.gov/sra/SRP153411).

Home modified by Kleber Padovani de Souza

Kleber Padovani de Souza — Wed, 01 Aug 2018 17:52:32 -0000

--- v17
+++ v18
@@ -1,6 +1,7 @@
-This project contains supplementary files used to produce the data presented in the paper entitled [Title of the paper](http://www.nature.com).
+This project contains supplementary files used to produce the data presented in the paper entitled [A metagenomic survey of soil microbial communities along a
+rehabilitation chronosequence after iron ore mining](https://www.nature.com/sdata/).

-Click [here](https://sourceforge.net/projects/corumba/files/) to download files. Other input files can be downloaded at NCBI website. Paired-end read files can be downloaded [here](https://www.ncbi.nlm.nih.gov/) and assembly files are available [here](https://www.ncbi.nlm.nih.gov/).
+Click [here](https://sourceforge.net/projects/corumba/files/) to download files. Other input files can be downloaded at NCBI website. Paired-end reads and contig files can be downloaded [here](https://www.ncbi.nlm.nih.gov/sra/SRP153411).

 We provide in folder **cluster_analysis** our source codes and additional files used to produce counting matrices of taxons and functions for clustering analysis listed below.

Home modified by Kleber Padovani de Souza

Kleber Padovani de Souza — Thu, 19 Jul 2018 13:40:29 -0000

--- v16
+++ v17
@@ -1,6 +1,6 @@
 This project contains supplementary files used to produce the data presented in the paper entitled [Title of the paper](http://www.nature.com).

-Click [here](https://sourceforge.net/projects/corumba/files/cluster_analysis/) to download files. Other input files can be downloaded at NCBI website. Paired-end read files can be downloaded [here](https://www.ncbi.nlm.nih.gov/) and assembly files are available [here](https://www.ncbi.nlm.nih.gov/).
+Click [here](https://sourceforge.net/projects/corumba/files/) to download files. Other input files can be downloaded at NCBI website. Paired-end read files can be downloaded [here](https://www.ncbi.nlm.nih.gov/) and assembly files are available [here](https://www.ncbi.nlm.nih.gov/).

 We provide in folder **cluster_analysis** our source codes and additional files used to produce counting matrices of taxons and functions for clustering analysis listed below.

Home modified by Kleber Padovani de Souza

Kleber Padovani de Souza — Thu, 19 Jul 2018 13:39:34 -0000

--- v15
+++ v16
@@ -2,7 +2,7 @@

 Click [here](https://sourceforge.net/projects/corumba/files/cluster_analysis/) to download files. Other input files can be downloaded at NCBI website. Paired-end read files can be downloaded [here](https://www.ncbi.nlm.nih.gov/) and assembly files are available [here](https://www.ncbi.nlm.nih.gov/).

-We provide here our source codes and additional files used to produce counting matrices of taxons and functions for clustering analysis listed below.
+We provide in folder **cluster_analysis** our source codes and additional files used to produce counting matrices of taxons and functions for clustering analysis listed below.

 Folder **inputs**: contains one file that is used as input for Kaiju (kaiju_input.tar.gz) and two other files that were generated by Kaiju and Interpro tools and were used to generate counting matrices by the corresponding scripts.

@@ -16,4 +16,9 @@
 * functional_analysis.R: produces the functional matrix
 * functional_cluster_plot.R: plots samples clustered by functions

+Additionaly, we provide the following supplementary files in folder **supplementary**:
+
+* quality: HTML files corresponding to quality reports of each read sample file obtained by FastQC tool (README.txt file contains a brief explanation about each report)
+* SoilSamples.csv: a CSV file containing chemical metadata about each soil sample
+
 If you have any trouble with these files, contact us by [someemail@itv.org](mailto:someemail@itv.org).

Home modified by Kleber Padovani de Souza

Kleber Padovani de Souza — Mon, 16 Jul 2018 15:11:18 -0000

--- v14
+++ v15
@@ -4,16 +4,16 @@

 We provide here our source codes and additional files used to produce counting matrices of taxons and functions for clustering analysis listed below.

-Folder **inputs**: contains two files, that were generated by Kaiju and Interpro tools and were used to generate counting matrices by the corresponding scripts.
+Folder **inputs**: contains one file that is used as input for Kaiju (kaiju_input.tar.gz) and two other files that were generated by Kaiju and Interpro tools and were used to generate counting matrices by the corresponding scripts.

 Folder **output**: contains the expected counting matrices output for the scripts.

 Folder **scripts**: contains five R scripts, described below:    

-* taxonomicanalysis.R: produces the taxonomic matrix
-* taxonomicclusterplot.R: plots samples clustered by taxonomic composition
-* taxonomicstackedplot.R: plots taxonomic composition of each sample
-* functionalanalysis.R: produces the functional matrix
-* functionalclusterplot.R: plots samples clustered by functions
+* taxonomic_analysis.R: produces the taxonomic matrix
+* taxonomic_cluster_plot.R: plots samples clustered by taxonomic composition
+* taxonomic_stacked_plot.R: plots taxonomic composition of each sample
+* functional_analysis.R: produces the functional matrix
+* functional_cluster_plot.R: plots samples clustered by functions

 If you have any trouble with these files, contact us by [someemail@itv.org](mailto:someemail@itv.org).

Home modified by Kleber Padovani de Souza

Kleber Padovani de Souza — Wed, 06 Jun 2018 23:33:46 -0000

--- v13
+++ v14
@@ -1,4 +1,4 @@
-This project contains supplementary files used to produce data presented in the paper entitled [Title of the paper](http://www.nature.com).
+This project contains supplementary files used to produce the data presented in the paper entitled [Title of the paper](http://www.nature.com).

 Click [here](https://sourceforge.net/projects/corumba/files/cluster_analysis/) to download files. Other input files can be downloaded at NCBI website. Paired-end read files can be downloaded [here](https://www.ncbi.nlm.nih.gov/) and assembly files are available [here](https://www.ncbi.nlm.nih.gov/).

Home modified by Kleber Padovani de Souza

Kleber Padovani de Souza — Wed, 06 Jun 2018 23:33:04 -0000

--- v12
+++ v13
@@ -5,7 +5,9 @@
 We provide here our source codes and additional files used to produce counting matrices of taxons and functions for clustering analysis listed below.

 Folder **inputs**: contains two files, that were generated by Kaiju and Interpro tools and were used to generate counting matrices by the corresponding scripts.
+
 Folder **output**: contains the expected counting matrices output for the scripts.
+
 Folder **scripts**: contains five R scripts, described below:    

 * taxonomicanalysis.R: produces the taxonomic matrix

Home modified by Kleber Padovani de Souza

Kleber Padovani de Souza — Wed, 06 Jun 2018 23:32:36 -0000

--- v11
+++ v12
@@ -7,6 +7,7 @@
 Folder **inputs**: contains two files, that were generated by Kaiju and Interpro tools and were used to generate counting matrices by the corresponding scripts.
 Folder **output**: contains the expected counting matrices output for the scripts.
 Folder **scripts**: contains five R scripts, described below:    
+
 * taxonomicanalysis.R: produces the taxonomic matrix
 * taxonomicclusterplot.R: plots samples clustered by taxonomic composition
 * taxonomicstackedplot.R: plots taxonomic composition of each sample

Home modified by Kleber Padovani de Souza

Kleber Padovani de Souza — Wed, 06 Jun 2018 23:32:19 -0000

--- v10
+++ v11
@@ -5,9 +5,8 @@
 We provide here our source codes and additional files used to produce counting matrices of taxons and functions for clustering analysis listed below.

 Folder **inputs**: contains two files, that were generated by Kaiju and Interpro tools and were used to generate counting matrices by the corresponding scripts.
-Folder **output**: contains the expected counting matrices output for the scripts
-    Folder **scripts**: contains five R scripts, described below:
-    
+Folder **output**: contains the expected counting matrices output for the scripts.
+Folder **scripts**: contains five R scripts, described below:    
 * taxonomicanalysis.R: produces the taxonomic matrix
 * taxonomicclusterplot.R: plots samples clustered by taxonomic composition
 * taxonomicstackedplot.R: plots taxonomic composition of each sample