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Commits on Dec 5, 2024

• fixed issue with older anndata versions

  HAL9032

  committed
  9606066

Commits on Nov 15, 2024

• adjusted anndata import in accordance to future warning

  HAL9032

  committed
  5e5c383

• fixed issue with numpy nan in _bld_met_mtx.py

  HAL9032

  committed
  0cface5

Commits on May 1, 2024

• removed display from motif enrichment

  HAL9032

  committed
  0498043

• added dpi parameter and minor fix for saving figures of motif enrichment plot

  HAL9032

  committed
  a51ea2f

Commits on Apr 12, 2024

• added annotate_peaks and helper fns

  HAL9032

  committed
  1a39ba4

• resolved issue with parameters in pp.pca

  HAL9032

  committed
  7ed3b08

• changed inplace .clip() in fns peak_mtx and gene_activity_mtx

  HAL9032

  committed
  2d80778

Commits on Apr 8, 2024

• new count mtx fns based on interval tree

  HAL9032

  committed
  ddc149c

Commits on Mar 21, 2024

• multiple testing correction in motif_enrichment and finalized plot_motif_enrichment wrapper fn

  HAL9032

  committed
  1650ca3

Commits on Feb 7, 2024

• added general plot_enrichment fn and plot_motif_enrichment wrapper fn; small changes in saving results in motif_enrichment

  HAL9032

  committed
  9d90353

• changed size of flank region considered for score calculation in get_scores fn

  HAL9032

  committed
  f7f957c

• bug fix in plot_footprints_compact; plotting additional info and minor adjustments in plot_footprints and plot_footprints_compact

  HAL9032

  committed
  fd65777

• search_motifs fn computes and stores number of tfbs per tf

  HAL9032

  committed
  72d78d8

• changed default fpr threshold in search_motifs fn

  HAL9032

  committed
  6d10d65

• added plot_footprints_compact fn; adjustments for plot_footprints fn; saving group_mapping during tn5 activity calculation

  HAL9032

  committed
  ba44b0a

Commits on Jan 31, 2024

• added motif_enrichment fn

  HAL9032

  committed
  61a2016

Commits on Jan 30, 2024

• moved binary_motif_mtx fn to enrichment analysis

  HAL9032

  committed
  7469325

Commits on Jan 29, 2024

• added binary_motif_mtx fn

  HAL9032

  committed
  939f93e

Commits on Jan 25, 2024

• added peak seq annotation, motif search, and footprinting

  HAL9032

  committed
  a940ea5

Commits on Dec 12, 2023

• Merge branch 'gtf_fix'

  HAL9032

  committed
  0e845ef

Commits on May 9, 2023

• Minor typo fix

  Show description for 070a946
  AtaiDobrynin

  authored
  070a946

Commits on Mar 13, 2023

• fixed bug with thresholds equal zero in set_filter

  HAL9032

  committed
  a2daf62

Commits on Mar 9, 2023

• removed temporary logging in tss_enrichment

  HAL9032

  committed
  702728e

• temporary logging in tss_enrichment

  HAL9032

  committed
  dc105e2

• added source parameter in tss_enrichment

  HAL9032

  committed
  8770b71

Commits on Feb 23, 2023

• minor fix

  HAL9032

  committed
  4c02b4e

• gene_activity_mtx: support for alternative keys in GTF file attr col

  HAL9032

  committed
  66efa54

Commits on Dec 5, 2022

• minor extension of previous commit

  HAL9032

  committed
  6190edf

• added consideration of header in BED input of peak_mtx

  HAL9032

  committed
  c045e8b

Commits on Dec 2, 2022

• axis labels for show_filters fn

  HAL9032

  committed
  a2505ce

Commits on Nov 30, 2022

• providing a list of valid barcodes for count mtx calculation is now optional

  HAL9032

  committed
  da0f563

• minor improvements to count matrix fns

  HAL9032

  committed
  0971cb4

• fixed feature sorting issue in count matrix fns

  HAL9032

  committed
  94440da

Commits on Nov 21, 2022

• Merge pull request #131 from crsct/master

  Show description for 6957a8a
  

  Anna Danese

  authored
  6957a8a

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