late 2020 release

• scHicClusterMinHash:
  • Adding umap
• adding option to color scatter plots with pre-classified information
• add scHicClusterMinHashHyperopt to
• adding scHicCorrelate
• scHicPlotConsensusMatrix:
  • fixing a bug which lead to a small last interaction matrix plot
• scHicManageSCool:
  • option to create a scool file given a scool file and a list of to be extracted matrices
• scHicConvertFormat:
  • option to write out sparse matrix text files
• add scHicTxtToSCool: able to import sparse text files as created by Ramani's bin_schic

Summer 2020 release bug fix 1

• Add saveMemory option
• Catching the possibility of a deadlock if too much data is loaded with too less cores
• Fixing the documentation

Summer 2020 release

• Better clustering with MinHash: More accurate, faster loading times, less memory, additional PCA
• In general: Fast loading of matrices. This version is up to 19 times faster (10 kb matrices scHiCExplorer version 4: 58 minutes. Version 5: < 3 minutes)
• Support for scool format as defined with version 0.8.9 of cooler
• scHicManageScool: Tool to update old scool (version 4 or less of scHiCExplorer) to new version. Option to extract a matrix to a single cool
• scHicConvertFormat: Tool to convert a scool matrix to the file and folder structure scHiCluster needs
• Option to plot PC1 vs PC2 on cluster results for scHicCluster and scHicClusterMinHash
• scHicClusterMinHash: New additional cluster algorithms: birch, agglomerative (ward, average, single, complete)
• scHicCluster and scHicClusterMinHash: Option to work on intra-chromosomal data only
• Multiple bug fixes
• Improved plotting of scHicPlotConsensusMatrices and scHicPlotClusterProfile

March 2020 release II

• Fixing a bug in scHicDemultiplex
• Improving the documentation on how to download the FASTQ files for example.

March 2020 release

Release 3:

• Change datatype name mcool to scool.
• Change tool scHicMergeToMCool to scHicMergeToSCool
• Add tool scHicCreateBulkMatrix to create the bulk matrix out of the individual single-cell matrices
• Improve the docs

Late winter 2020

• scHicClusterMinHash has a new parameter to control the share of rows which is transferred to C++ at once. This helps to reduce the memory footprint.
• Needs sparse-neighbors-search version 0.5

Late fall 2019

The first release of the single-cell HiCExplorer (scHiCExplorer) provides methods to demultiplex, manipulate, analyse and visualize single-cell Hi-C data.

• Demultiplex
• Create mcool matrices based on n cool matrices from hicBuildMatrix
• Adjust matrix and changes the resolution
• Cluster the samples with different techniques and dimension reduction methods
• Plot cluster profiles and consensus matrices