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Commits on Dec 5, 2024

• fixed issue with older anndata versions

  HAL9032

  committed
  9606066

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Commits on Nov 15, 2024

• adjusted anndata import in accordance to future warning

  HAL9032

  committed
  5e5c383

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• fixed issue with numpy nan in _bld_met_mtx.py

  HAL9032

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  0cface5

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Commits on May 1, 2024

• removed display from motif enrichment

  HAL9032

  committed
  0498043

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

  HAL9032

  committed
  a51ea2f

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Commits on Apr 12, 2024

• added annotate_peaks and helper fns

  HAL9032

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  1a39ba4

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• resolved issue with parameters in pp.pca

  HAL9032

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  7ed3b08

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

  HAL9032

  committed
  2d80778

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Commits on Apr 8, 2024

• new count mtx fns based on interval tree

  HAL9032

  committed
  ddc149c

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Commits on Mar 21, 2024

• multiple testing correction in motif_enrichment and finalized plot_motif_enrichment wrapper fn

  HAL9032

  committed
  1650ca3

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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

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

  HAL9032

  committed
  f7f957c

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

  HAL9032

  committed
  fd65777

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• search_motifs fn computes and stores number of tfbs per tf

  HAL9032

  committed
  72d78d8

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• changed default fpr threshold in search_motifs fn

  HAL9032

  committed
  6d10d65

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

  HAL9032

  committed
  ba44b0a

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Commits on Jan 31, 2024

• added motif_enrichment fn

  HAL9032

  committed
  61a2016

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Commits on Jan 30, 2024

• moved binary_motif_mtx fn to enrichment analysis

  HAL9032

  committed
  7469325

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Commits on Jan 29, 2024

• added binary_motif_mtx fn

  HAL9032

  committed
  939f93e

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Commits on Jan 25, 2024

• added peak seq annotation, motif search, and footprinting

  HAL9032

  committed
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Commits on Dec 12, 2023

• Merge branch 'gtf_fix'

  HAL9032

  committed
  0e845ef

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Commits on May 9, 2023

• Minor typo fix

  Show description for 070a946
  AtaiDobrynin

  authored
  070a946

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Commits on Mar 13, 2023

• fixed bug with thresholds equal zero in set_filter

  HAL9032

  committed
  a2daf62

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Commits on Mar 9, 2023

• removed temporary logging in tss_enrichment

  HAL9032

  committed
  702728e

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• temporary logging in tss_enrichment

  HAL9032

  committed
  dc105e2

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• added source parameter in tss_enrichment

  HAL9032

  committed
  8770b71

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Commits on Feb 23, 2023

• minor fix

  HAL9032

  committed
  4c02b4e

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

  HAL9032

  committed
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Commits on Dec 5, 2022

• minor extension of previous commit

  HAL9032

  committed
  6190edf

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• added consideration of header in BED input of peak_mtx

  HAL9032

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Commits on Dec 2, 2022

• axis labels for show_filters fn

  HAL9032

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Commits on Nov 30, 2022

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

  HAL9032

  committed
  da0f563

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• minor improvements to count matrix fns

  HAL9032

  committed
  0971cb4

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• fixed feature sorting issue in count matrix fns

  HAL9032

  committed
  94440da

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Commits on Nov 21, 2022

• removed unnecessary suffixes from import statements

  crsct

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