News

** 4 Dezember 2020**

Release of version 7:

  • scHicClusterMinHash:

    • Adding umap

    • adding option to color scatter plots with pre-classified information

  • add scHicClusterMinHashHyperopt

  • 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

  • scHicTxtToSCool: able to import sparse text files as created by Ramani’s bin_schic

** 11 August 2020**

Release of version 6:

  • Add saveMemory option

  • Catching the possibility of a deadlock if too much data is loaded with too less cores

  • Fixing the documentation

** 5 August 2020**

Release of version 5:

  • 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

** 8 March 2020**

Release of version 4:

  • Fixing a bug in scHicDemultiplex

  • Improving the documentation on how to download the FASTQ files for example.

7th March 2020

Release of version 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

24th February 2020

Release of version 2.

  • Option to define how many nearest neighbors in scHicCluster or scHicClusterMinHash should be computed

  • scHicClusterMinHash: Partially loading of data from Python to C++ to decrease memory footprint to a 1/4.

30th November 2019

Release of version 1 of the single-cell HiCExplorer.

06th November 2019

Creation of the single-cell HiCExplorer documentation.