GSEA.jl
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The official command-line program for gene-set-enrichment analysis (GSEA) 🏔️
The official command-line program for gene-set-enrichment analysis (GSEA) 🏔️
Quick Start
1. Go to example
directory
cd example/sarcopenia
ls -l
2. Make an output directory
mkdir ~/Downloads/gsea
3. Run GSEA
gsea metric-rank \
~/Downloads/gsea \
target_x_sample_x_number.tsv \
feature_x_sample_x_number.tsv \
set_features.json \
--number-of-permutations 10 \
--more-sets-to-plot "WP_DNA_MISMATCH_REPAIR WP_CELL_CYCLE ALIEN"
4. Look at the results
cd ~/Downloads/gsea
ls -l
head -3 *.tsv
open *.html
Use gsea
command-line interface
Run metric-rank
(standard) GSEA
gsea metric-rank
Run user-rank
(pre-rank) GSEA
gsea user-rank
Run data-rank
(single-sample) GSEA
gsea data-rank
Convert .cls
and .gct
to .tsv
s
gsea convert-cls-gct
Convert one or more .gmt
s to a .json
gsea convert-gmt
Use in julia
]add
]add https://github.com/KwatMDPhD/GSEA.jl
Use
Each command-line-interface command has a corresponding function. Options and flags are keyword arguments.
Reproduce Quick Start in julia
using GSEA
const DI = joinpath("example", "sarcopenia")
GSEA.metric_rank(
mkpath(joinpath(homedir(), "Downloads", "gsea")),
joinpath(DI, "target_x_sample_x_number.tsv"),
joinpath(DI, "feature_x_sample_x_number.tsv"),
joinpath(DI, "set_features.json"),
number_of_permutations = 10,
more_sets_to_plot = ["WP_DNA_MISMATCH_REPAIR", "WP_CELL_CYCLE", "ALIEN"],
)
Install
-
Download the latest release and extract it.
-
Path
PATH=$(pwd)/gsea/bin:$PATH
- Use
We plan to sign the app soon. Meanwhile, enable 3rd-party apps on your macOS.
gsea --help
🎉
Build
If installation is unavailable or fails, try building.
1. Download
git clone https://github.com/KwatMDPhD/GSEA.jl
2. Instantiate
cd GSEA.jl &&
julia --project --eval "using Pkg; Pkg.instantiate()"
3. Build
julia --project deps/build.jl app tarball
4. Path
PATH=$(pwd)/build/gsea/bin:$PATH
5. Use
gsea --help
🎊
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