v0.3.2

Hotfix: fixed path in get_refsample()

v0.3.1

Hotfix for unexpected behavior in conda dependencies

v0.3.0

• updated documentation

• comfort:

  • added geneIDs to WPS/COV/STARTs and FFT tables

• snakefile_GE_analysis:

  • added background normalization
  • ported FFT calculation to python
  • separated multiple steps for increased maintainability

• snakefile_WPS:

  • restructured file paths
  • moved window extension to separate
  • moved WPS padding correction to extractFromBAM_RegionBed_WPS_Cov.py

• GE_unsupervised:

  • added rules for generating clusterings and heatmaps between all samples of an experiment using FFT intensities
    • kmeans clustering
    • HDBSCAN clustering
    • heatmaps
    • clustermaps (heatmap with hierarchical clustering)

v0.2.1

v0.2.1

• bugfix paths
• simplified path handling in plotting scripts
• improved readability of label files

v0.2.0

refactor

• changed config.yml to example.config.yml
• updated schemas
• updated Documentation

new files

• updated blacklists for both genome builds
• updated genome files for both genome builds

new feature

• snakefile_GE_analysis:

  • updated ProteinAtlas
    • 3 types: Blood, Tissue, Tissue+cell-lines
  • added support for GRCh38

• snakefile_WPS:

  • added support for normalization by random background sequences
    • generate random background sequences not overlapping target regions
    • calculate WPS,COV,STARTS table for background sequences

• extractFromBAM_RegionBed_WPS_Cov.py

  • added output for fragment endpoints (STARTS output)
  • added strand specificity

• overlays.py:

  • integrated normalization by background sequences

v0.1.2

• Updated documentation for config files(fixes #3)

• Updated overlays.py (resolves #1)

  • adding samples is now wrapped in a function
  • flanking regions are now determined dynamically

• added CHANGELOG.md