gseapy-v0.9.13

Bump version

gseapy-v0.9.12

Enrichr module:

1. Support modEnrich (https://amp.pharm.mssm.edu/modEnrichr/) .
   Add organism argument. Now, Human, Mouse, Fly, Yeast, Worm, Fish are supported.
2. background argument bug fixed, #66 .
   Now, background type could be: list, tuple, set, Series, ndarray, int, a txt file or biomart dataset name.

gseapy-v0.9.9

1. Add new module biomart: Convert gene ids using BioMart API
2. Fixed heatmap bug in gsea output.
3. Support custom gene set input for enrichr. Hypergeometric test using scipy
4. Fixed other small issues

gseapy-v0.9.8

Highlight

1. Visualization improvement for gseaplot, barplot, dotplot, heatmap. Now these function could be used in python console. see Examples for details.
2. Leading edge genes now output to the results.
3. Fixed small bugs in v0.9.5

gseapy-v0.9.5

Important
Please note : from version 0.9.5 on, GSEApy only works on Python 3.4+ and Python 2.x will no longer be supported. For a Python 2 version you can install v0.9.4.

• Now, set outdir=None, there will be not any output files on your hard disk. Usefull inside python console. #43

• GSEA,Prerank,ssGSEA api improvement

  • gene_sets now support input type: dict. This is usefull when use your own gene_sets builded in python console. gene_sets dict looks like this:

    gene_sets = {
    "gene_set_1": ["gene_A", "gene_B", ...],
    "gene_set_2": ["gene_B", "gene_C", ...],
    ...
    "gene_set_100": ["gene_A", "gene_T", ...]
    }

• enrichr api improvment

  • gene_sets now support input type: list, str. see details: here
  • fixed loop break when enrichr server block the connection if you have large amount of queries

• small bugs in ssgsea

v0.9.4

Last version support Python2

• improve barplot output style
• fixed logging issues when used in another package #44
• enrichr: multi-libraries input support.

v0.9.3

Most stable version so far.

• fixed memory error when Input data generate big 3D numpy array. #39
• improved docs

v0.9.2

This version still cause memory error, when using gsea with big array.

All existed APIs will no be deleted any longer.

New feature:

• add no_plot keyword to all modules to skip plotting
  • this is useful only if output data are interested
  • also useful when re-run your analysis by skip plotting
• docs are more clear now, particularly ssgsea
  • ssgsea output file improvement.
  • see docs and Examples

v0.9.1

Note: if you have limited RAM (1 core needs 1G), use v0.8.11.

• Fixed stack overflow bug in module ssgsea with v0.9.0.
  • drop high dimensional numpy array for computing while using ssgsea, but need more running time.
  • ssgsea source code: revert back to old version of 0.8.11, which with multiprocessing support.

Notes about ssGSEA

• ES values from ssgsea are consistent with GSVA:gsva(method='ssgsea'), see here.

• download comparison.zip and, run these two files to compare gseapy.ssgsea and GSVA:gsva(method='ssgsea')

  • test.ssgesa.gseapy.py
  • test.ssgesa.R.r

comparison.zip

v0.9.0

Next generation of GSEApy

ssgsea using too much memory. Please use >=0.9.1

• Using high dimension numpy arrays to accelerate computation.
• drop multiprocessing, but reserved the keyword argument for future development.
• docs more clear
• APIs and internal structure of gseapy become more consistent and easier to maintain.
• minor bugs fixed