Update docs

Author: mrueda

README.md

@@ -14,7 +14,7 @@
 [![Docker Pulls](https://badgen.net/docker/pulls/manuelrueda/pheno-ranker?icon=docker&label=pulls)](https://hub.docker.com/r/manuelrueda/pheno-ranker/)
 [![Docker Image Size](https://badgen.net/docker/size/manuelrueda/pheno-ranker?icon=docker&label=image%20size)](https://hub.docker.com/r/manuelrueda/pheno-ranker/)
 [![Documentation Status](https://github.com/cnag-biomedical-informatics/pheno-ranker/actions/workflows/documentation.yml/badge.svg)](https://github.com/cnag-biomedical-informatics/pheno-ranker/actions/workflows/documentation.yml)
-[![License: Artistic-2.0](https://img.shields.io/badge/License-Artistic%202.0-0298c3.svg)](https://opensource.org/licenses/Artistic-2.0)
+[![License](https://img.shields.io/badge/License-Artistic%202.0-0298c3.svg)](https://opensource.org/licenses/Artistic-2.0)
 [![Google Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1n3Etu4fnwuDWNveSMb1SzuN50O2a05Rg)
 
 ---
@@ -122,7 +122,7 @@ To ensure Perl recognizes your local modules every time you start a new terminal
 
     echo 'eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib)' >> ~/.bashrc
 
-To **update** to the newest version (showing commands for Option 2):
+To **update** to the newest version:
 
     cpanm Pheno::Ranker
 

bin/pheno-ranker

@@ -364,7 +364,7 @@ To ensure Perl recognizes your local modules every time you start a new terminal
 
   echo 'eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib)' >> ~/.bashrc
 
-To B<update> to the newest version (showing commands for Option 2):
+To B<update> to the newest version:
     
   cpanm Pheno::Ranker
 

docs/csv-import.md

@@ -36,7 +36,7 @@
         | foo1 | bar1a,bar1b | baz1 |
         | foo2 | bar2a,bar2b | baz2 |
         
-        Column `Bar` is an array and columns `Foo`and `Baz` aren't. Your file does not have a column that can be used as an **identifier** for each row.
+        Column `Bar` is an array and columns `Foo` and `Baz` aren't. Your file does not have a column that can be used as an **identifier** for each row.
         
         OK, we are going to use the included [utility](https://raw.githubusercontent.com/CNAG-Biomedical-Informatics/pheno-ranker/main/utils/csv2pheno_ranker/README.md) to convert `example.csv`:
         

docs/implementation.md

@@ -36,7 +36,7 @@ graph LR
 
 `Pheno-Ranker` includes several utilities:
 
-1. [bff-pxf-plot](./bff-pxf-plot.md) to create summary statistcs for BFF/PXF data.
+1. [bff-pxf-plot](./bff-pxf-plot.md) to create summary statistics for BFF/PXF data.
 2. [bff-pxf-simulator](./bff-pxf-simulator.md) to simulate BFF/PXF data.
 3. [csv2pheno-ranker](./csv-import.md) to enable using `Pheno-Ranker` with `CSV`.
 4. [QR encoder/decoder](./qr-code-generator.md) to transform data (back and forth) into QR codes and `PDF` reports.

docs/phenopackets-corpus.md

@@ -24,7 +24,7 @@ jq -s '.' $(ls -1 */*/*.json | shuf -n 1000) > combined.json
 
 ??? Note "About reproducibility"
 
-    We used `0.1.20`. You can reproduce this example with the folowing list of files:
+    We used `0.1.20`. You can reproduce this example with the following list of files:
 
     ```bash
     --8<-- "data/combined.txt"

docs/pxf.md

@@ -9,7 +9,7 @@ Phenopackets organize information using [top-level elements](https://phenopacket
 
 ??? Tip "Browsing PXF `JSON` data"
 
-    You can browse a public Phenopackets v2 file with onf of the following **JSON viewers**:
+    You can browse a public Phenopackets v2 file with one of the following **JSON viewers**:
 
     * [JSON Hero](https://jsonhero.io/new?url=https://raw.githubusercontent.com/cnag-biomedical-informatics/convert-pheno/main/t/pxf2bff/in/pxf.json)
     * [Datasette](https://lite.datasette.io/?json=https%3A%2F%2Fraw.githubusercontent.com%2Fcnag-biomedical-informatics%2Fconvert-pheno%2Fmain%2Ft%2Fomop2pxf%2Fout%2Fpxf.json#/data?sql=select+*+from+pxf)
@@ -20,7 +20,7 @@ When using the `pheno-ranker` command-line interface, simply ensure the [correct
 
 ??? Question "What happens with deeply nested arrays such as `interpretations.diagnosis.genomicInterpretations`?"
 
-    The property [genomicInterpretation](https://phenopacket-schema.readthedocs.io/en/latest/genomic-interpretation.html) presents some peculiarities for several reasons. It can have multiple nested levels or arrays, the key `"id"` may refer to a given patient, plus the key `subjectOrBiosampleId` referes to the same patient too!. This implies that users might be interested in the variants, but since patient ids will be in the flattened key, it will never match another patient.
+    The property [genomicInterpretation](https://phenopacket-schema.readthedocs.io/en/latest/genomic-interpretation.html) presents some peculiarities for several reasons. It can have multiple nested levels or arrays, the key `"id"` may refer to a given patient, plus the key `subjectOrBiosampleId` refers to the same patient too!. This implies that users might be interested in the variants, but since patient ids will be in the flattened key, it will never match another patient.
 
     `Pheno-Ranker` will handle this for you for the term `interpretations`. The approach taken is to transition from **array** data structures to **objects**.
 

docs/tcga-clinical.md

@@ -10,9 +10,9 @@ This guide explains how to use `Pheno-Ranker` with data from [TCGA](https://port
 
 1. We are going to perform a data download by visiting the following link: [Cohort Builder](https://portal.gdc.cancer.gov/analysis_page?app=CohortBuilder&tab=general)
 
-2. In Project, select a few named **TCGA**. Then click in "CASES" and switch to **Table View**. 
+2. In Project, select a few named **TCGA**. Then click on "CASES" and switch to **Table View**. 
 
-3. Next, click in **TSV** to download the data. You will likely end up with a file like: `clinical.cohort.2025-06-02.tar.gz`.
+3. Next, click on **TSV** to download the data. You will likely end up with a file like: `clinical.cohort.2025-06-02.tar.gz`.
 
 ```bash
 # Change the filename to match yours!
@@ -70,7 +70,7 @@ exclude_variables_regex: 'datetime|days_to_|cases.case_id|cases.submitter_id|dem
 
 !!! Warning "Quantitative data"
 
-    In this exercise, we have decided to get rid of numerical data. In a real example, we would have created **bins for quantitative variables**.
+    In this exercise, we have decided to exclude numerical data. In a real example, we would have created **bins for quantitative variables**.
 
 Now run the calculation again: