From fa50628014f0f163f2ed5ea2b038d6d70defc8d7 Mon Sep 17 00:00:00 2001 From: John Elizarraras Date: Thu, 25 Apr 2024 16:27:38 -0500 Subject: [PATCH] update readmes and remove examples --- .gitignore | 2 ++ README.md | 4 +++- src/main.rs | 4 ---- test.json | 1 - test.txt | 1 - webgestalt_lib/README.md | 3 ++- 6 files changed, 7 insertions(+), 8 deletions(-) delete mode 100644 test.json delete mode 100644 test.txt diff --git a/.gitignore b/.gitignore index 76a75fb..49cd174 100644 --- a/.gitignore +++ b/.gitignore @@ -20,3 +20,5 @@ ref.txt target_symbols.txt /*.gmt /*.rnk +test.json +test.txt \ No newline at end of file diff --git a/README.md b/README.md index 0cf5c21..f7eb57a 100644 --- a/README.md +++ b/README.md @@ -10,6 +10,8 @@ This CLI is focused purely on computation. **It does not provide GMT files or HT ## Install +Requires the [rust toolchain](https://rustup.rs/). Then run the following command in your terminal: + ```shell cargo install webgestalt ``` @@ -25,5 +27,5 @@ webgestalt --help Example of running over-representation analysis using `kegg.gmt`, with an interesting list at `int.txt` and a reference of `ref.txt`. Outputs JSON file at `output.json` ```shell -ora -g kegg.gmt -i int.txt -r ref.txt -o output.json +webgestalt ora -g kegg.gmt -i int.txt -r ref.txt -o output.json ``` \ No newline at end of file diff --git a/src/main.rs b/src/main.rs index 18ca42f..8d3da10 100644 --- a/src/main.rs +++ b/src/main.rs @@ -10,10 +10,6 @@ use webgestalt_lib::methods::nta::NTAConfig; use webgestalt_lib::methods::ora::ORAConfig; use webgestalt_lib::readers::utils::Item; use webgestalt_lib::readers::{read_gmt_file, read_rank_file}; - -/// WebGestalt CLI. -/// ORA and GSEA enrichment tool. -/// Created by John Elizarraras from the Bing Zhang Lab. #[derive(Parser)] #[command(author, version, about, long_about = None)] struct CliArgs { diff --git a/test.json b/test.json deleted file mode 100644 index 439a77e..0000000 --- a/test.json +++ /dev/null @@ -1 +0,0 @@ -{"neighborhood":["FGB","SERPINE1","SPON2","COL5A1","FN1","LOX","FKBP10","COL5A2","FSTL1","BMP1","PCOLCE","HTRA1","THBS2","COL12A1","CLU","COL1A2","THBS1","SERPINF1","COL3A1","ADAMTS12","COL1A1","SPARC","ITGA5","COL6A3","SRPX2","AEBP1","IGFBP3","CTHRC1","MXRA5","PLOD1","PXDN","VTN","PLOD2","ANGPTL2","SERPINH1","FGA","C1R","EMILIN1","SULF1","PRSS23","OAF","FAP","CPB2","MMP14","TGFBI","LAMA4","COL6A2","P3H1","P4HA2","C6"],"scores":[0.003562641692883106,0.003538995831327317,0.0035261170000374393,0.003520964848069161,0.003453101120580822,0.003417249145657785,0.0033766597115792345,0.0033652148198500924,0.0033505622162513645,0.003344459790139319,0.0033199543202775553,0.0032971161674534,0.0032562224317521193,0.003214976052318932,0.0031988135105238506,0.003173961059615259,0.003136971779695295,0.0031292778427251377,0.003083775791844985,0.003079872169312326,0.003054806567355033,0.003051717960542315,0.0030333842454479554,0.0030191113074753413,0.0030029019070158137,0.002997246602418623,0.002991653792861727,0.0029775872240226375,0.002976624696451578,0.0029631394227223494,0.0029529885636102693,0.0029421174392407837,0.0029223935545971682,0.002922177526399187,0.0029119959073008973,0.0029022993560898734,0.0028955153609407014,0.0028919839702413004,0.002880182115917173,0.0028481800800364346,0.0028451928311296693,0.002824056975349717,0.0027969515922297307,0.002795980580116232,0.0027956753168207876,0.0027939714666224487,0.002764482075775976,0.0027474523294589515,0.0027429130067067138,0.0027403889075339007],"candidates":[]} \ No newline at end of file diff --git a/test.txt b/test.txt deleted file mode 100644 index 9c4b2dc..0000000 --- a/test.txt +++ /dev/null @@ -1 +0,0 @@ -{"neighborhood":["LOXL2"],"scores":[0.5039114522916316],"candidates":["LOXL2"]} \ No newline at end of file diff --git a/webgestalt_lib/README.md b/webgestalt_lib/README.md index ad64cc1..60385c2 100644 --- a/webgestalt_lib/README.md +++ b/webgestalt_lib/README.md @@ -8,13 +8,14 @@ Supported methods include: - Over-Representation Analysis (ORA) - Gene Set Enrichment Analysis (GSEA) +- Network topology-based analysis (NTA) ## Installation To use webgestalt_lib in your Rust project, add the following line to your `Cargo.toml`. ```toml -webgestalt_lib = "0.2.0" # change to wanted version +webgestalt_lib = "0.3.0" # change to wanted version ``` If you are just interested in running an analysis, rather than develop new tools, please use one of the packages mentioned at the beginning of the README.