triqler - v0.7.3

• Fix DIA prior fitting matplotlib dependency
• Weaken pandas version requirement to >=1.4.0

- Python
Published by MatthewThe over 2 years ago

triqler - v0.7.2

• Replace multiprocessing_pool by job-pool package
• Update version retrieval
• First unit test
• Linting

- Python
Published by MatthewThe over 2 years ago

triqler - v0.7.1

v0.07.1 * Add file list mapping functionality to DIA-NN converter (#20)

- Python
Published by MatthewThe almost 3 years ago

triqler - v0.7

v0.07 * Added option to estimate hyperparameter priors for DIA data * Added DIA-NN to triqler converter * Added pandas as dependency for DIA prior * Clean up sub-packages (#19)

- Python
Published by MatthewThe almost 3 years ago

triqler - v0.6.4

• Fixed csv fieldsizelimit function call (#17)
• Added poetry environment

- Python
Published by MatthewThe over 3 years ago

triqler - v0.6.3

• List comprehensions replaced with numpy methods for some quick gains (#16)
• Up the CSV field size limit (#16)

- Python
Published by MatthewThe over 3 years ago

triqler - v0.6.2

• Added limit to number of cores for qvality (#13)

- Python
Published by MatthewThe about 4 years ago

triqler - v0.6.1

v0.06.1 * Added lower bound estimate based on sigmaProtein and numSamples

- Python
Published by MatthewThe about 5 years ago

triqler - v0.6

v0.06 * Added posterior heatmap plots for lists of protein IDs * Added --use-gene-names option for MaxQuant converter

- Python
Published by MatthewThe over 5 years ago

triqler - v0.5

v0.05 * Updates to dinosaur converter * Added plotting flags for posterior plots

- Python
Published by MatthewThe over 5 years ago

triqler - v0.4

v0.04 * Experimental support for MaxQuant MBR * Added Dinosaur converter * Fixed some converter scripts Python 3 compatibility (#12) * Fixed problem with standalone percolator input for dinosaur converter * Add support for disabling multithreading (by setting --num_threads 1)

- Python
Published by MatthewThe over 5 years ago

triqler - v0.3.1

v0.03.1 * Added issued command to log * Fixed MaxQuant converter with fractionated data (#10) * Fixed small issues with posterior distribution package

- Python
Published by MatthewThe over 5 years ago

triqler - v0.3

v0.03 * Added support for converting Quandenser and MaxQuant results to Triqler input format (#5) * Added support for printing posterior distributions to a file * Added support for plotting posterior distributions and hyperparameter estimation fits

- Python
Published by MatthewThe over 6 years ago

triqler - v0.2.1

v0.02.1 * Fixed problems with CSV reading and writing on Windows (#9) * Fixed lambda function pickling problem with multiprocessing on Windows (#8)

- Python
Published by MatthewThe almost 7 years ago

triqler - v0.02

v0.02 * Fixed empty columns as extra proteins issue (#4) * Improved logging messages * Optimizations for very large datasets. Replaced some operations on python lists by their numpy equivalents to speed up calculation on larger datasets. Also, we now skip the posterior calculation for proteins with identification PEP = 1.0, since they will never be differentially abundant anyway.

- Python
Published by MatthewThe almost 7 years ago

triqler - v0.01.4

v0.01.4 * Fixed windows multiprocessing error more elegantly (#2) * Suppressed warnings from child processes (#3)

- Python
Published by MatthewThe over 7 years ago

triqler - v0.01.3

v0.01.3 * Fixed Windows multiprocessing error (#2) * Added spectrum identifier to peptide output

- Python
Published by MatthewThe over 7 years ago

triqler - v0.01.2

v0.01.2 * Bumped numpy dependency to 1.12 for numpy.countnonzero along axis * Removed need for condidx:condname format for condition column * Set --minsamples option to 2 instead of 1 and added check for --min_samples >= 2 * Added filter for entries with 0 or NaN intensity * Added run dependent identification PEP for consensus spectra

- Python
Published by MatthewThe over 7 years ago

triqler - v0.01.1

v0.01.1 * Fixed dependency on qvality (#1) * Changed to (slightly slower) 2D integration for in-group variance latent variable.

- Python
Published by MatthewThe almost 8 years ago

triqler - v0.01.0

v0.01.0 * Initial release

- Python
Published by MatthewThe almost 8 years ago