agartland / fishersapi Goto Github PK
View Code? Open in Web Editor NEWA package that for applying a fast implementation of Fisher's exact test to observations in a pandas DataFrame.
License: MIT License
A package that for applying a fast implementation of Fisher's exact test to observations in a pandas DataFrame.
License: MIT License
Hello!
Thanks so much for putting all of the effort into re-factoring tcrdist2
! The pre-processing workflows are a lovely addition as well. While trying to follow the default installation instructions using conda
, I ran into several minor issues. The first is that the pip install
calls for fishersapi
and fisher
both kept failing out repeatedly. To circumvent this, I put together the following conda env
which can be used with conda create -f tcrdist2.yaml
:
name: tcrdist2
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=0_gnu
- ca-certificates=2019.11.28=hecc5488_0
- certifi=2019.11.28=py38_0
- cycler=0.10.0=py_2
- dbus=1.13.6=he372182_0
- expat=2.2.9=he1b5a44_2
- fisher=0.1.9=py38hc1659b7_0
- fontconfig=2.13.1=h86ecdb6_1001
- freetype=2.10.0=he983fc9_1
- future=0.18.2=py38_0
- gettext=0.19.8.1=hc5be6a0_1002
- glib=2.58.3=py38h6f030ca_1002
- gst-plugins-base=1.14.5=h0935bb2_1
- gstreamer=1.14.5=h36ae1b5_1
- icu=64.2=he1b5a44_1
- joblib=0.14.1=py_0
- jpeg=9c=h14c3975_1001
- kiwisolver=1.1.0=py38hc9558a2_0
- ld_impl_linux-64=2.33.1=h53a641e_8
- libblas=3.8.0=14_openblas
- libcblas=3.8.0=14_openblas
- libclang=9.0.1=default_hde54327_0
- libffi=3.2.1=he1b5a44_1006
- libgcc-ng=9.2.0=h24d8f2e_2
- libgfortran-ng=7.3.0=hdf63c60_4
- libgomp=9.2.0=h24d8f2e_2
- libiconv=1.15=h516909a_1005
- liblapack=3.8.0=14_openblas
- libllvm9=9.0.1=hc9558a2_0
- libopenblas=0.3.7=h5ec1e0e_6
- libpng=1.6.37=hed695b0_0
- libstdcxx-ng=9.2.0=hdf63c60_2
- libuuid=2.32.1=h14c3975_1000
- libxcb=1.13=h14c3975_1002
- libxkbcommon=0.9.1=hebb1f50_0
- libxml2=2.9.10=hee79883_0
- matplotlib=3.1.2=py38_1
- matplotlib-base=3.1.2=py38h250f245_1
- ncurses=6.1=hf484d3e_1002
- nspr=4.24=he1b5a44_0
- nss=3.47=he751ad9_0
- numpy=1.17.5=py38h95a1406_0
- openssl=1.1.1d=h516909a_0
- pandas=1.0.0=py38hb3f55d8_0
- patsy=0.5.1=py_0
- pcre=8.43=he1b5a44_0
- pip=20.0.2=py38_1
- pthread-stubs=0.4=h14c3975_1001
- pyparsing=2.4.6=py_0
- pyqt=5.12.3=py38hcca6a23_1
- python=3.8.1=h357f687_2
- python-dateutil=2.8.1=py_0
- pytz=2019.3=py_0
- qt=5.12.5=hd8c4c69_1
- readline=8.0=hf8c457e_0
- scikit-learn=0.22.1=py38hcdab131_1
- scipy=1.4.1=py38h921218d_0
- seaborn=0.9.0=py_2
- setuptools=45.1.0=py38_0
- six=1.14.0=py38_0
- sqlite=3.30.1=hcee41ef_0
- statsmodels=0.11.0=py38h516909a_0
- tk=8.6.10=hed695b0_0
- tornado=6.0.3=py38h516909a_0
- wheel=0.34.2=py38_0
- xorg-libxau=1.0.9=h14c3975_0
- xorg-libxdmcp=1.1.3=h516909a_0
- xz=5.2.4=h14c3975_1001
- zlib=1.2.11=h516909a_1006
- pip:
- fishersapi==0.1.dev0
- parasail==1.1.19
- pyqt5-sip==4.19.18
- pyqtwebengine==5.12.1
- tcrdist2==2.0.dev0
prefix: /path/to/anaconda3/envs/tcrdist2
I hope this will help other conda
users get off the ground and running quickly!
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