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r-bioinformatics
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edgePy
A Python implementation of edgeR for differential expression analysis
https://edgepy.readthedocs.io
MIT License
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Restarting edgePy
#82
bc2zb
opened
1 year ago
0
What happened to this? was this project abandoned? =(
#81
pabloacera
opened
1 year ago
5
Fix norm fn sigs
#80
zbohannan
opened
5 years ago
0
Use consistent interface to tpm and rpkm
#79
moritzschaefer
opened
5 years ago
1
Refactor DGEList.get_gene_mask_and_lengths. Should go into CanonicalDataStore
#78
moritzschaefer
opened
5 years ago
0
Fix LaTeX formatting for method tpm()
#77
clintval
closed
5 years ago
2
Fix LaTeX formatting on method tpm()
#76
clintval
closed
5 years ago
0
Af rpkm
#75
apfejes
closed
5 years ago
1
Update tox to python 3.7
#74
moritzschaefer
closed
5 years ago
5
Af ensembl
#73
apfejes
closed
5 years ago
1
implemented TPM normalization
#72
moritzschaefer
closed
5 years ago
1
Develop introductory documentation and tutorial
#71
michaeljhatch
opened
5 years ago
0
Link to smart_open documentation in our docs
#70
apfejes
closed
6 years ago
0
Convert table to restructured text
#69
sdhutchins
closed
6 years ago
0
Make an RST table
#68
clintval
closed
6 years ago
5
Missing `--cov` for pytest config
#67
clintval
opened
6 years ago
0
Fix several docstrings still in NumPy format, by converting to google…
#66
apfejes
closed
6 years ago
0
Auto build Sphinx documentation
#65
apfejes
closed
6 years ago
0
Doctests are not being run
#64
clintval
opened
6 years ago
0
Logging implementation
#63
sdhutchins
closed
6 years ago
3
Use Logging instead of print for scripts/edgepy.py
#62
apfejes
closed
6 years ago
1
Normalization methods should return a new DGEList instance
#61
apfejes
closed
3 years ago
10
Example RNAseq Analysis
#60
eegk
closed
6 years ago
1
Clean up dgelist from import
#59
apfejes
closed
6 years ago
1
Basic functionality for running a DGE experiment.
#58
apfejes
closed
6 years ago
0
A functioning KS test for comparing distributions.
#57
apfejes
closed
6 years ago
2
Testing CPM and a few bugfixes along the way
#56
apfejes
closed
6 years ago
4
Fix Docstrings in edgePy folder.
#55
apfejes
closed
6 years ago
1
read_handle() needs to strip off non-genes from data import
#54
apfejes
closed
6 years ago
9
Em black
#53
edmundmiller
closed
6 years ago
1
Add documentation for io submodule
#52
Carbyne
closed
5 years ago
6
Update CONTRIBUTING.md - line length
#51
apfejes
closed
6 years ago
1
Change zipfile decompression to use smart_open library (fixes #49)
#50
Carbyne
closed
6 years ago
3
Use smart_open library to transparently decompress files
#49
Carbyne
closed
6 years ago
0
Fix #47
#48
edmundmiller
closed
6 years ago
1
Do not support developing on system environment
#47
clintval
closed
6 years ago
0
Updated setup.cfg as per pull request.
#46
veena-v-g
closed
6 years ago
3
Cannot have space in `.cfg` key
#45
clintval
closed
6 years ago
1
This addresses #41 - adding a warning in the Readme that this is stil…
#44
apfejes
closed
6 years ago
1
Switch to using 119 characters per line, instead of 99.
#43
apfejes
closed
6 years ago
2
Should this project be called "edgepy" over "edgePy"
#42
clintval
opened
6 years ago
7
Issue warning in README that this is still prototype and un-released
#41
clintval
closed
6 years ago
1
Testing DGE_list, and a Mongo Integration
#40
apfejes
closed
6 years ago
4
Simple validation for issue #38
#39
julianstanley
closed
6 years ago
8
DGEList samples and counts property validation
#38
julianstanley
opened
6 years ago
0
Wrap all dynamic/static analysis tools in tox
#37
clintval
closed
6 years ago
2
WIP: Wrapped all static tools in Tox and included dev venv builder
#36
clintval
closed
6 years ago
0
Change license to MIT in setup.py (Closes #32)
#35
Carbyne
closed
6 years ago
1
Create headers of functions/classes
#34
vzg100
opened
6 years ago
3
cleaned up root directory
#33
michaeljhatch
closed
6 years ago
3
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