NEWS.md

In snikumbh/archR: Identify Different Architectures of Sequence Elements

archR 0.1.8

New features

• Custom ordering of individual clusters within collated clusters. Earlier this followed label ordering as per cutree output
• Improved messages for model selection using cross-validation
• (User-facing) The agglomeration and distance method used for collation of clusters can be set as part of configuration settings

Breaking changes

• (User-facing) Argument name inner_chunk_size changed to chunk_size in archR_set_config()

archR 0.1.7

New features

• Accounting and correcting for over-fitting improves clusters/architectures' quality
• Improved messages
• (User-facing) New function collate_clusters()

Breaking changes

• (User-facing) tolerance no longer an argument in archR_set_configuration

archR 0.1.6

New features

• Can choose to fix aspect ratio for visualization functions
• plot_ggheatmap()
• plot_ggseqlogo()
• viz_bas_vec_heatmap_seqlogo()
• viz_bas_vec_heatmap()
• viz_bas_vec_seqlogo()
• plot_arch_for_clusters()
• plot_ggseqlogo_of_seqs()
• Ability to detect occurrence of just for sake clustering when fetching from HAC

archR 0.1.5

New features

• (User-facing) Getter functions to fetch archR result object elements.
• seqs_str() to fetch DNA sequences for a particular cluster, iteration etc.
• get_clBasVec() to fetch basis vectors element at given iteration.
• get_clBasVec_k() to fetch number of basis vectors/clusters.
• get_clBasVec_m() to fetch basis vectors.
• get_seqClLab() to fetch cluster Ids for each sequence.

Breaking changes

• (User-facing) Arguments of all functions consistently use underscores.

archR 0.1.2

Bug fixes

• Fix staged installation error. This enables seamless installation on macOS.

New features

• CI with GHA.
• (User-facing) archR result list has new elements:
• timeInfo if timeFlag is TRUE;
• clustSol storing combined clusters from the last iteration of archR.
• (User-facing) Architectures/clusters sequence logos can be plotted with auto y-axis limits for information content (0-max instead of 0-2).
• (User-facing) TFBSTools moved from dependency to suggests. This eases installation of archR by reducing possibility of failed installation.

archR 0.99.3

New features

• Accepts FASTA sequences as DNAStringSet object(s)

snikumbh/archR documentation built on July 5, 2021, 8:46 a.m.