Skip to content

Latest commit

 

History

History
81 lines (49 loc) · 2.21 KB

ChangeLog.md

File metadata and controls

81 lines (49 loc) · 2.21 KB

v1.3.0 (2021-07-18)

  • First offcial release of the single-cell ATAC-seq pipeline.
  • A lot of improvments to single-cell analysis pipeline.
  • Create signal enrichment bigwig files for the ATAC-seq pipeline.
  • Bug fix: #19

v1.2.1 (2020-06-27)

  • Much faster data downloading from GEO by using fasterq-dump when available.

  • Change peak merging algorithm in single cell ATAC-seq analysis.

  • Add bwa_seed_length to the configuration.

  • Fix worker pool exhaustion when processes being killed unexpectedly.

  • bug fix: #5

v1.2.0 (2020-05-03)

Breaking changes:

  • Need to include the index prefix when specifying the location of the BWA or RSEM index in config.yml. For example: (old) path-to-index/bwa_index => (new) path-to-index/bwa_index/GRCh38.fa.

Other changes:

  • Add the option to input "Filtered" Bam files in ATAC-seq.

  • The Taiji is now shipped with C igraph library (no need to install it separately).

  • Add basic input validations.

  • Implement the chromVAR algorithm in single cell ATAC analysis.

  • Bug fixes.

v1.1.0 (2020-01-10)

  • Auto-detect effective genome size for MACS2.

  • Compress BAM files generated by BWA.

  • Reduce memory usage in certain steps.

  • Fix the normalization issue in bigwig file generation.

  • Add more features to single cell RNA-seq analysis pipeline.

  • Add more features to single cell ATAC-seq analysis pipeline.

v1.0.1 (2019-10-14)

This release introduces a lot of new functions, performance improvements and bug fixes.

  • Use promoter accessibility to estimate the gene expression when RNA-seq is not available. This greately improves the results.

  • New interface for Parallelism and distributed computing which supports running jobs on PBS or slurm. The number of jobs and resource usage of each step can now be configured.

  • Add more QCs and visualization, including fragment size distribution, TSS enrichment, signal correlation and so on.

  • Preliminary support for single cell RNA and ATAC analysis.

v0.5.0 (2018-10-28)

  • Add a function to include external networks, using the field external_network in the configuration file.