Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

GitHub / frankligy / SNAF

Splicing Neo Antigen Finder (SNAF) is an easy-to-use Python package to identify splicing-derived tumor neoantigens from RNA sequencing data, it further leverages both deep learning and hierarchical Bayesian models to prioritize certain candidates for experimental validation

JSON API: https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/frankligy%2FSNAF

Stars: 32
Forks: 6
Open Issues: 16

License: mit
Language: Python
Repo Size: 86.6 MB
Dependencies: 363

Created: over 2 years ago
Updated: 15 days ago
Last pushed: about 1 month ago
Last synced: 1 day ago

Commit Stats

Commits: 260
Authors: 2
Mean commits per author: 130.0
Development Distribution Score: 0.031
More commit stats: https://commits.ecosyste.ms/hosts/GitHub/repositories/frankligy/SNAF

Files

Readme

Dependencies

AltAnalyze/requirements_all.txt pypi

Babel ==2.6.0
BeautifulSoup ==3.2.1
BiBench ==0.1
Bottleneck ==0.7.0
CIRCexplorer2 ==2.3.6
CITE-seq-Count ==1.2
CacheControl ==0.11.7
ConfigArgParse ==0.13.0
Cython ==0.27.2
Django ==1.8.4
Fabric ==1.14.0
Flask ==0.12.2
FlowCytometryTools ==0.4.6
GoreUtilities ==0.5.0
HTSeq ==0.6.1
Jinja2 ==2.7.3
MACS ==1.4.2
MACS2 ==2.1.1.20160309
Mako ==1.0.1
Markdown ==2.2.0
MarkupSafe ==0.18
MySQL-python ==1.2.4b4
NucleoATAC ==0.3.4
PICRUSt ==1.0.0
PIL ==1.1.7
Pillow ==2.5.1
Pmw ==2.0.0
PyNaCl ==1.1.2
PyPDF2 ==1.26.0
PyVCF ==0.6.8
PyYAML ==3.12
Pygments ==2.2.0
RSeQC ==2.6.4
SQLAlchemy ==0.9.4
Sphinx ==1.7.5
Tenjin ==1.1.1
Theano ==0.8.2
Unidecode ==0.4.21
VCF-kit ==0.1.6
Werkzeug ==0.12.2
XlsxWriter ==1.2.9
aafigure ==0.6
alabaster ==0.7.11
annoy ==1.13.0
appdirs ==1.4.3
apptools ==4.4.0
args ==0.1.0
asn1crypto ==0.22.0
astroid ==1.1.1
atactk ==0.1.6
avro ==1.8.2
awesome-slugify ==1.6.5
backports-abc ==0.4
backports.functools-lru-cache ==1.5
backports.ssl-match-hostname ==3.5.0.1
bcrypt ==3.1.3
bd2k-python-lib ==1.14a1.dev37
beautifulsoup4 ==4.6.1
biased-stop-words ==2017.7.13.0
biom-format ==1.3.1
biopython ==1.64
bitarray ==0.8.1
bleach ==1.5.0
bob.spear ==1.1.2
bs4 ==0.0.1
bsddb3 ==6.2.1
burrito ==0.9.1
burrito-fillings ==0.1.1
bx-python ==0.7.3
certifi ==2017.4.17
cffi ==1.11.5
cget ==0.1.4
chardet ==3.0.4
click ==6.6
clint ==0.5.1
clipper ==0.2.0
cmd2 ==0.6.8
codacy-coverage ==1.3.11
cogent ==1.5.3
colorama ==0.3.9
colored ==1.3.93
configobj ==5.0.6
contextlib2 ==0.5.5
coverage ==4.5.1
cryptography ==2.3.1
cutadapt ==1.14
cwltest ==1.0.20170214185319
cwltool ==1.0.20170413194156
cycler ==0.10.0
cyvcf2 ==0.8.8
dask ==0.10.0
decorator ==4.3.0
deepTools ==3.1.0
dill ==0.2.5
dipy ==0.13.0
dnslib ==0.9.7
docopt ==0.6.1
docutils ==0.11
easybuild ==3.6.2
easybuild-easyblocks ==3.6.2
easybuild-easyconfigs ==3.6.2
easybuild-framework ==3.6.2
emperor ==0.9.51
enum34 ==1.0.4
envisage ==4.7.0
et-xmlfile ==1.0.1
export ==0.1.2
fastcluster ==1.1.11
fcsparser ==0.1.4
freetype-py ==0.4.1
funcsigs ==1.0.2
functools32 ==3.2.3.post2
future ==0.13.1
futures ==3.1.1
gdata ==2.0.18
gdc-client ==1.4.0
genmod ==1.7.9
h5py ==2.8.0
hashlib ==20081119
html5lib ==0.9999999
idna ==2.5
igraph ==0.1.11
imagesize ==1.0.0
interval-tree ==0.3
intervaltree ==3.0.2
ipaddress ==1.0.18
ipykernel ==4.2.1
ipyparallel ==5.0.1
ipython ==4.0.0
ipython-cluster-helper ==0.5.1
ipython-genutils ==0.1.0
ipywidgets ==4.1.1
isodate ==0.5.4
itsdangerous ==0.24
javabridge ==1.0.14
jdcal ==1.3
jsonpickle ==0.7.1
jsonschema ==2.6.0
junit-xml ==1.7
jupyter ==1.0.0
jupyter-client ==4.1.1
jupyter-console ==4.0.3
jupyter-core ==4.0.6
kiwisolver ==1.0.1
leidenalg ==0.7.0
llvmlite ==0.29.0.dev0
lockfile ==0.12.2
logilab-common ==0.62.0
louvain ==0.6.1
lxml ==4.2.1
mahotas ==1.2.1
matplotlib ==2.1.2
mayavi ==4.6.2
misopy ==0.5.3
mistune ==0.7.4
mock ==2.0.0
mpi4py ==1.3.1
mysql-connector-python-rf ==2.2.2
natsort ==3.5.6
nbconvert ==4.1.0
nbformat ==4.4.0
ndg-httpsclient ==0.5.0
netifaces ==0.10.4
networkx ==1.11
nfsometer ==1.8
ngsutils ==0.5.9
nibabel ==2.1.0
nimfa ==1.3.4
nipype ==0.12.1
nitime ==0.7
nltk ==3.0.1
nose ==1.3.7
notebook ==4.0.6
numba ==0.40.1
numexpr ==2.6.2
numpy ==1.14.6
numpydoc ==0.8.0
oligotyping ==2.0
openpyxl ==2.4.0
ordereddict ==1.1
packaging ==16.8
pandas ==0.23.4
paramiko ==2.2.1
path.py ==8.1.2
pathlib ==1.0.1
pathlib2 ==2.2.1
patsy ==0.5.1
pbr ==3.0.1
ped-parser ==1.1.2
pep8 ==1.5.7
pexpect ==4.0.1
pickleshare ==0.5
platform-python-lsf-api ==1.0.1
plinkio ==0.9.6
plotly ==2.7.0
plotting ==0.1.0
progressbar ==2.3
protobuf ==3.3.0
prov ==1.4.0
psutil ==2.1.1
ptyprocess ==0.5
py ==1.5.3
py2bit ==0.3.0
pyBigWig ==0.3.11
pyOpenSSL ==18.0.0
pyasn1 ==0.4.3
pybedtools ==0.7.6
pycairo ==1.14.0
pycparser ==2.12
pydicom ==0.9.9
pyface ==6.0.0
pyflakes ==0.8.1
pygsl ==0.9.5
pylint ==1.2.1
pymol ==1.4.0
pymorph ==0.96
pynast ==1.2.2
pyopencl ==2015.1
pyparsing ==2.3.0
pypez ==0.1.5
pyqi ==0.3.1
pysam ==0.15.0
pysftp ==0.2.9
pysqlite ==2.8.3
pytabix ==0.1
pytest ==2.7.2
pytest-cov ==2.5.1
python-Levenshtein ==0.12.0
python-bioformats ==1.0.9
python-dateutil ==2.7.3
python-igraph ==0.7.1.post6
python-louvain ==0.11
pytools ==2015.1.2
pytz ==2018.7
pyzmq ==15.1.0
qcli ==0.1.1
qiime ==1.8.0
qiime-default-reference ==0.1.3
qtconsole ==4.1.1
rdflib ==4.2.2
rdflib-jsonld ==0.4.0
regex ==2019.1.24
reportlab ==3.1.8
requests ==2.7.0
rope ==0.10.2
rpy2 ==2.8.5
rson ==0.9
ruamel.ordereddict ==0.4.9
ruamel.yaml ==0.15.7
scandir ==1.5
schema-salad ==2.5.20170328195758
scikit-bio ==0.2.3
scikit-image ==0.12.3
scikit-learn ==0.17
scipy ==0.19.0
seaborn ==0.8.1
sexpdata ==0.0.3
shellescape ==3.4.1
simplegeneric ==0.8.1
simplejson ==3.8.2
singledispatch ==3.4.0.3
six ==1.11.0
sklearn ==0.0
smartypants ==1.8.6
snowballstemmer ==1.2.1
sortedcontainers ==2.1.0
sphinxcontrib-websupport ==1.1.0
spp-idr ==0.0.1
statsmodels ==0.10.0
structural-dhcp-mriqc ==0.8.4a2
structural-dhcp-svg2rlg ==0.3
subprocess32 ==3.5.2
suds ==0.4
synapseclient ==1.2
tabulate ==0.8.2
termcolor ==1.1.0
terminado ==0.5
toil ==3.8.0
toolz ==0.8.0
tornado ==4.4.2
traitlets ==4.3.2
traits ==4.6.0
traitsui ==6.0.0
typing ==3.5.3.0
umap-learn ==0.3.6
urllib3 ==1.21.1
vcf-parser ==1.0
virtualenv ==13.0.3
vsc-base ==2.8.3
vsc-install ==0.11.2
vtk ==8.1.0
weblogo ==3.3
websockify ==0.8.0
wxPython-common ==3.0.2.0
xbob.sox ==1.1.0
xlrd ==1.0.0
xopen ==0.2.1
xvfbwrapper ==0.2.8
yahmm ==1.1.2
zc.buildout ==2.2.1

AltAnalyze/requirements_slim.txt pypi

Pillow ==2.5.1
annoy ==1.13.0
llvmlite ==0.29.0
matplotlib ==2.1.2
networkx ==1.11
nimfa ==1.3.4
numba ==0.40.1
numpy ==1.14.6
pandas ==0.23.4
pycairo ==1.14.0
pysam ==0.15.0
python-igraph ==0.7.1.post6
python-louvain ==0.11
requests ==2.7.0
scipy ==0.19.0
sklearn ==0.0
umap-learn ==0.3.6

docs/requirements.txt pypi

Werkzeug ==2.0.2
anndata ==0.7.6
biopython ==1.79
dash ==2.0.0
dash-core-components ==2.0.0
dash-dangerously-set-inner-html ==0.0.2
dash-html-components ==2.0.0
dash-table ==5.0.0
h5py ==2.10.0
lifelines ==0.26.4
mhcflurry ==2.0.5
mygene ==3.2.2
numba ==0.53.0
numpy ==1.18.5
pandas ==1.3.4
plotly ==5.4.0
readthedocs-sphinx-search ==0.1.0rc3
requests ==2.26.0
scipy ==1.4.1
seaborn ==0.11.2
sphinx ==4.1.1
sphinx-autoapi ==1.8.4
sphinx_rtd_theme ==0.5.2
statsmodels ==0.13.1
tensorflow ==2.3.0
tqdm ==4.62.3
umap-learn ==0.5.2
xmltodict ==0.12.0
xmltramp2 ==3.1.1

AltAnalyze/Dockerfile docker

python 2 build

AltAnalyze/requirements_slim_test.txt pypi

Pillow ==2.5.1 test
annoy ==1.13.0 test
llvmlite ==0.29.0 test
matplotlib ==2.1.2 test
networkx ==1.11 test
nimfa ==1.3.4 test
numba ==0.40.1 test
numpy ==1.14.6 test
pandas ==0.23.4 test
pycairo ==1.14.0 test
pysam ==0.15.0 test
python-louvain ==0.11 test
requests ==2.7.0 test
scipy ==0.19.0 test
sklearn ==0.0 test
umap-learn ==0.3.6 test

setup.py pypi