Merge branch 'master' of https://github.com/sfu-ireceptor/dataloading…

…-curation

test/imgt/README.md

@@ -8,21 +8,21 @@ This directory consists of a set of example IMGT HighV-QUEST annotated files and
 accompanying repertoire metadata files.
 
 A detailed description of using HighV-QUEST is beyond the scope of this
-document, for more details please visit the HighV-QUEST page
-(https://www.imgt.org/HighV-QUEST/home.action)
+document, for more details please visit the [HighV-QUEST page](
+https://www.imgt.org/HighV-QUEST/home.action)
 
 # Examples
 
 There is a single data set in this directory
-that consists of eight repertoires and is a subset of the data from the paper "Immunoglobulin class-switched B cells provide an active immune axis between CNS and periphery in multiple sclerosis" by Palanichamy et. al.
-(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4176763/). The data set was curated using the iReceptor Data Curation process listed here: http://www.ireceptor.org/curation. The full data set from this study is available through the iReceptor Scientific Gateway (http://gateway.ireceptor.org).
+that consists of eight repertoires and is a subset of the data from the paper ["Immunoglobulin class-switched B cells provide an active immune axis between CNS and periphery in multiple sclerosis"](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4176763/) by Palanichamy et. al.
+ The data set was curated using the [iReceptor Data Curation process](http://www.ireceptor.org/curation). The full data set from this study is available through the [iReceptor Scientific Gateway](http://gateway.ireceptor.org).
 
 The directory consists of 
 a iReceptor Repertoire metadata file (a UTF-8 encoded CSV file) and a set of rearrangement files.
 Each repertiore has been annotated with the HighV-QUEST annotation
 tool and the directory contains a single rearrangement file (a single .txz file) for each
 repertoire. 
-If you are using an iReceptor Turnkey Repository (https://github.com/sfu-ireceptor/turnkey-service-php) please refer to the loading data section of the iReceptor Turnkey documentation for more detailed instructions on load Repertoire metadata and Rearrangement files.
+If you are using an [iReceptor Turnkey Repository](https://github.com/sfu-ireceptor/turnkey-service-php) please refer to the loading data section of the iReceptor Turnkey documentation for more detailed instructions on loading Repertoire metadata and Rearrangement files.
 
 
 

test/mixcr-clone/README.md

@@ -3,9 +3,9 @@ This directory contains test clone data annotated by the MiXCR annotation tool.
 
 # Example Data
 
-The example data in this directory is a small subset of the data from the paper "[Next-Generation Sequencing of T and B Cell Receptor Repertoires from COVID-19 Patients Showed Signatures Associated with Severity of Disease](https://doi.org/10.1016/j.immuni.2020.06.024) from Schultheiß et al. The data set consists of a set of sequence annotations and clones from a single repertoire from this study. As such, it should only be considered in the context of a test data set and it should not be considered a representative sample of the data from this study. The data set was curated using the iReceptor Data Curation process listed here: http://www.ireceptor.org/curation. The data set, in its entirety, is available through the iReceptor Scientific Gateway (http://gateway.ireceptor.org).
+The example data in this directory is a small subset of the data from the paper "[Next-Generation Sequencing of T and B Cell Receptor Repertoires from COVID-19 Patients Showed Signatures Associated with Severity of Disease](https://doi.org/10.1016/j.immuni.2020.06.024) from Schultheiß et al. The data set consists of a set of sequence annotations and clones from a single repertoire from this study. As such, it should only be considered in the context of a test data set and it should not be considered a representative sample of the data from this study. The data set was curated using the [iReceptor Data Curation process](http://www.ireceptor.org/curation). The data set, in its entirety, is available through the [iReceptor Scientific Gateway](http://gateway.ireceptor.org).
 
 The example data set consists of two data files. The first file is a repertoire metadata file, as a UTF-8 encoded CSV file. The file consists of a header line, which contains the field names that will be written to the repository, followed by a single metadata line for a single repertoire from the above study. In a typical repertoire metadata file, there would be a single line for each repertoire in the study. The second file is a clone file for this repertoire, as annotated using the MiXCR annotation tool. The file is a typical annotation output file from MiXCR.
 
-Please refer to the loading data section of the iReceptor Turnkey documentation (https://github.com/sfu-ireceptor/turnkey-service-php) on how to load this data into and iReceptor Turnkey repository.
+Please refer to the loading data section of the [iReceptor Turnkey documentation](https://github.com/sfu-ireceptor/turnkey-service-php) on how to load this data into an iReceptor Turnkey repository.