Changelog

0.10.2

  • Fixed readthedocs

  • Removed save_memory from LIONESS (CLI). The first PANDA needs to keep the PANDA value in memory

  • Added BONOBO to CLI

0.10.1

  • Added BONOBO to docs.

  • Added LIONESS examples to docs.

  • Fixed mistake in README.

0.10.0

  • Added BONOBO to the zoo!

  • Cobra has been updated and integrated with PANDA.

0.9.16

  • Added COBRA to the zoo!

  • We no longer costrain the igraph version to be older than 0.10. This will probably change the community assignment results, but the upgrade has been recommended by the igraph developers.

0.9.13

  • We have added some options to LIONESS: single lioness files can be saved in HDF (fmt=’h5’) which saves a lot of time and memory. By passing ignore_final to lioness (with save_single_lioness) each lioness is discarded after being saved, hence you won’t have all lioness networks in memory at the same time.

  • PANDA can be run with_header from CLI

  • Added pytables/tables in dependencies.

0.9.12

  • We are changing the PANDA outputs and default flags. For now we are updating the command line

call only, behavior is kept as in 0.9.11 for the internal functions. By passing old_compatible = False the final output will always have column headers and indices.

  • PUMA and PANDA do not save_tmp as default.

  • lioness for puma has been fixed

  • Fixed PANDA data preprocessing bug

0.9.11 (2022-11-04)

  • Added LIONESS for DRAGON with tests

  • PANDA preprocessing expression: In Panda preprocessing there was a problem with indices. Using gene2idx.get(x, 0) always give you the index 0 if x is missing fro

m gene2idx.get (like a gene in gene expression and not in motif, since gene2idx is build on top of the intersection of expression and motif). Now we use gene_names to both create the indices for self.expression and to access with .loc[] the expression data frame self.expression_data - New PANDA tests - Updated LIONESS start and end parameters so that they are independent of the background. Example: One can now run panda on 100 samples

and then apply LIONESS on only the first 10.

  • Added LIONESS subset parameter: passing subset parameters (a list of indices or sample names, [1,2,10]) allows to run LIONESS only on specific samples. This parameter has priority over the start and end parameters.

0.9.10 (2022-10-28)

  • Fixing single/double precision for GPU

  • Clearing GPU after computation to free more memory

0.9.9 (2022-10-21)

  • added the case for square nonsymmetric matrices for normalization in panda

  • Updated tests for panda and lioness to match MATLAB

  • Fixed Panda-Lioness GPU inconsistencies

  • Forcing igraph<0.10, otherwise community assignment results change. This will need further investigation for the future.

  • Fixed lioness GPU export (now lioness allows to save the full matrix, with explicit edge and sample names).

0.9.6 (2022-06-10)

  • Ligress filters PPI according to input motif

0.9.5 (2022-05-24)

  • Added output with sample names in Lioness

  • ligress sample names are setup as strings

  • correct order of motif prior in ligress

0.9.4 (2022-05-20)

  • First ligress release

  • solved puma bug

0.9.2 (2022-03-04)

  • added command line interface (panda, lioness)

  • updating documentation

0.9.0 (2022-02-11)

  • we fixed the panda-lioness and puma-lioness behavior ( panda was passing the updated motif to lioness ). The results are now compatible with the ones of netzooR.

  • removed py3.6 support

  • updated version on anaconda.org

0.8.0 (2021-06-08)

  • support for Python v3.9

  • addition of DRAGON + unit tests +tutorial and many bug fixes that Daniel and Marouen have been doing as a user requests

0.7.2 (2020-07-18)

  • PANDA reads arguments as dataframes in addition to file paths

  • changed condor ground truth to match output of python-igraph 0.8.2.

0.7.1 (2020-06-27)

  • Major fix for OTTER behavior across platforms.

0.7.0 (2020-01-18)

  • new tool: OTTER

  • unit test for OTTER

  • fix for PANDA force field

  • tweaks for compatibility of gpuPANDA with cupy

0.6.2 (Stockholm) (2020-05-15)

  • Added gpuPANDA, which is a gpu-accelerated implementation of PANDA

  • Added gpuLIONESS

  • Added a gpuPANDA and gpuLIONESS tutorial

  • Fixed condor dependency to python-igraph (still under investigation in #82 )

0.6.1 (2020-01-18)

  • sambar tutorial

  • condor tutorial

  • added 3.8 to Ubunutu test server (along with 3.6 and 3.7 )

  • Created three options for data processing in PANDA.
    • Union: adds rows for genes/TFs that are missing in at least one prior (expression, ppi, motif)

    • Intersection: removes TF/genes that missing in at least one prior

    • Legacy: previous data processing behavior

  • The default was set to union in netZooM, netZooR, netZooPy as it is the default in netZooC.

0.5.0 (2019-11-22)

  • pysambar

0.4.0 (2019-11-18)

  • pycondor

0.3.0 (2019-11-14)

  • pypuma

0.2.0 (2019-11-13)

  • pylioness

0.1.1 (2019-9-3)

  • fixed call to save_memory=True

0.1.0 (2019-7-26)

  • transition to python 3

  • Changelog added to the doc

  • pypanda: original import and NaN values in normalized matrices are replaced with values normalized by the overall z-score. This allows running the Toy Data provided in this repository.