fix: Global change CMA-Lab > TCP-Lab

README.md

@@ -1,7 +1,7 @@
 # Transportome Profiler analysis
 
 This repository contains the code for the analysis on the expression profile of
-the transportome in Cancer based on the [MTP-DB](https://github.com/CMA-Lab/MTP-DB).
+the transportome in Cancer based on the [MTP-DB](https://github.com/TCP-Lab/MTP-DB).
 
 This is a two-step process. The database is queried for information by the
 script in `src/geneset_maker`. The algorithm generates gene sets ready for use
@@ -17,7 +17,7 @@ You can run the analysis in two ways: locally or in a Docker container.
 In both cases, you must first clone and link the repository locally:
 ```bash
 # Clone the repo
-git clone [email protected]:CMA-Lab/transportome_profiler.git
+git clone [email protected]:TCP-Lab/transportome_profiler.git
 cd ./transportome_profiler
 # Make housekeeping directories. See the following note.
 ./link A_FOLDER_THAT_WILL_CONTAIN_THE_DATA

makefile

@@ -77,7 +77,7 @@ $(data_dir)/in/selected_metadata:
 # TODO2: once we publish, change this to point at a static tag again.
 $(local_mtpdb):
 	mkdir -p $(@D)
-	wget -O $@.tar.gz https://github.com/CMA-Lab/MTP-DB/releases/latest/download/MTPDB.sqlite.gz --inet4-only
+	wget -O $@.tar.gz https://github.com/TCP-Lab/MTP-DB/releases/latest/download/MTPDB.sqlite.gz --inet4-only
 	tar -xvzf $@.tar.gz -C $(@D)
 	mv $(data_dir)/in/MTPDB_v0.23.17-beta.sqlite $@
 	rm $@.tar.gz

paper/src/sections/010_introduction.tex

@@ -58,9 +58,9 @@ \section{Introduction}
 After sorting all the protein-coding genes found in cancer cells based on their differential expression with respect to healthy cells, we ran a pre-ranked \gls{gsea} on these ordered lists to obtain enrichment scores for every \gls{tgs}.
 We therefore obtained the ``dysregulation status'' of most functional facets of the transportome in $19$ different cancer tissue types.
 
-We provide an open-source, documented, and reproducible Python package, Daedalus (\href{https://github.com/CMA-Lab/MTP-DB}{github.com/CMA-Lab/MTP-DB}) that retrieves transportome-related data from various databases and compiles it in a local \mono{.sqlite} database.
+We provide an open-source, documented, and reproducible Python package, Daedalus (\href{https://github.com/TCP-Lab/MTP-DB}{github.com/TCP-Lab/MTP-DB}) that retrieves transportome-related data from various databases and compiles it in a local \mono{.sqlite} database.
 In parallel, we also provide pre-compiled database files as periodic releases.
 
-A \mono{make}-driven and docker-containerized pipeline, named ``transportome profiler'', (\href{https://github.com/CMA-Lab/transportome_profiler}{github.com/CMA-Lab/transportome\_profiler}) is also available.
+A \mono{make}-driven and docker-containerized pipeline, named ``transportome profiler'', (\href{https://github.com/TCP-Lab/transportome_profiler}{github.com/TCP-Lab/transportome\_profiler}) is also available.
 It takes gene expression data and the aforementioned database to generate gene sets, sorts genes based on their differential expression, and runs \gls{gsea}.
 This pipeline was designed with modularity and reproducibility in mind, so that it would be easily adaptable on other datasets and databases.

paper/src/sections/020_MnMs.tex

@@ -83,10 +83,10 @@ \subsection{The Membrane Transport Protein Database}
 The thesaurus is contained in a single, human-readable comma-separated-values file, available in the remote repository.
 
 The \gls{mtpdb} will be an effective way to stimulate further research in the Transportome by providing a centralized and human- and machine-friendly place to obtain a lot of relevant information on Transportome genes.
-The pre-compiled \gls{mtpdb} and the Daedalus package are open-source and available for free on GitHub at \href{https://github.com/CMA-Lab/MTP-DB/}{www.github.com/CMA-Lab/MTP-DB}, and we encourage users to inspect and propose improvements.
+The pre-compiled \gls{mtpdb} and the Daedalus package are open-source and available for free on GitHub at \href{https://github.com/TCP-Lab/MTP-DB/}{www.github.com/TCP-Lab/MTP-DB}, and we encourage users to inspect and propose improvements.
 
 At every development milestone, a published version of the database (in the form of the generated SQLite file) will be released on GitHub, for reproducibility purposes.
-The latest release can be downloaded directly from \href{https://github.com/CMA-Lab/MTP-DB/releases/latest/download/MTPDB.sqlite.gz}{this URL} in \mono{gzipped} format.
+The latest release can be downloaded directly from \href{https://github.com/TCP-Lab/MTP-DB/releases/latest/download/MTPDB.sqlite.gz}{this URL} in \mono{gzipped} format.
 Additionally, note that the data blob downloaded and then used by Daedalus to generate the database is locally saved as a Python Pickle file, and is the only file that the package needs to regenerate the database.
 This can be useful to exactly reproduce the database in the future even after the remote databases have updated.
 The database is versioned using the CalVer specification, with representation \mono{Major.YY.0W[\_MINOR][-TAG]}.
@@ -190,7 +190,7 @@ \subsection{The Membrane Transport Protein Database}
 
 An overview of the database schema, with information on the type of data in every table, can be seen in Table \ref{tab:databaseSchema}.
 The actual database schema file is present in the GitHub repository at
-\href{https://github.com/CMA-Lab/MTP-DB/blob/main/src/db_rebuilder/daedalus/local_data/schema.sql}{this URL}.
+\href{https://github.com/TCP-Lab/MTP-DB/blob/main/src/db_rebuilder/daedalus/local_data/schema.sql}{this URL}.
 
 \subsection{Generation of Transporter Gene Lists}
 
@@ -274,7 +274,7 @@ \subsection{GSEA analysis}
 
 To pair the healthy and tumor data together, we therefore followed the macroscopic grouping provided by the metadata files in the Xena platform.
 To subset the very large expression matrix file based on the metadata, we implemented a Python package called \textit{metasplit}, which makes use of the low level Rust-compiled \mono{xsv} package to speed up the computation \todo{PUT A REFERENCE HERE}.
-The specific calls used to subset the expression matrix and therefore match the tumor and healthy samples are available in the GitHub repository at \href{https://github.com/CMA-Lab/transportome_profiler/blob/main/src/run_dea/tcga_gtex_queries.json}{this url}. %Should we explicitly show them as a table??
+The specific calls used to subset the expression matrix and therefore match the tumor and healthy samples are available in the GitHub repository at \href{https://github.com/TCP-Lab/transportome_profiler/blob/main/src/run_dea/tcga_gtex_queries.json}{this url}. %Should we explicitly show them as a table??
 As an overview, we compared tumor samples with their healthy counterparts from the same tissue or organ of origin.
 
 % Is the following correct? -- We might want to talk about this later, or earlier.

paper/src/sections/999_other_metadata.tex

@@ -20,9 +20,9 @@ \subsection{Author Contributions}
 \subsection{Data and Code Availability}
 Combined TCGA and GTEX data and metadata is available from the Xena platform at
 \href{https://toil-xena-hub.s3.us-east-1.amazonaws.com/download/TcgaTargetGtex_gene_expected_count.gz }{this url} and \href{https://toil-xena-hub.s3.us-east-1.amazonaws.com/download/TcgaTargetGTEX_phenotype.txt.gz}{this url}.
-The MTP-DB is available on GitHub at \href{https://github.com/CMA-Lab/MTP-DB}{CMA-Lab/MTP-DB}.
+The MTP-DB is available on GitHub at \href{https://github.com/TCP-Lab/MTP-DB}{TCP-Lab/MTP-DB}.
 The full analysis code as well as \mono{LaTeX} code to generate the author
-manuscript is available on GitHub at \href{https://github.com/CMA-Lab/transportome_profiler}{CMA-Lab/transportome\_profiler}.
+manuscript is available on GitHub at \href{https://github.com/TCP-Lab/transportome_profiler}{TCP-Lab/transportome\_profiler}.
 
 \subsection{Conflicts of Interest}
 The Authors declare no conflicts of interest.