https://github.com/nsalomonis/altanalyze

AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.
https://github.com/nsalomonis/altanalyze

alternative-splicing bam-files bioinformatics-pipeline cell-cycle cell-type-classification clustering command-line-tool fastq-anaysis graphical-interface louvain-community-detection marker-gene-analysis network-analysis pagerank pathway-analysis python rna-seq-data scrna-seq-data single-cell-splicing splicing-quantification splicing-visualization

Last synced: 23 days ago
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AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.

• Host: GitHub
• URL: https://github.com/nsalomonis/altanalyze
• Owner: nsalomonis
• License: apache-2.0
• Created: 2015-08-08T02:00:53.000Z (almost 9 years ago)
• Default Branch: master
• Last Pushed: 2022-07-07T23:10:36.000Z (almost 2 years ago)
• Last Synced: 2024-05-20T03:03:43.676Z (about 1 month ago)
• Topics: alternative-splicing, bam-files, bioinformatics-pipeline, cell-cycle, cell-type-classification, clustering, command-line-tool, fastq-anaysis, graphical-interface, louvain-community-detection, marker-gene-analysis, network-analysis, pagerank, pathway-analysis, python, rna-seq-data, scrna-seq-data, single-cell-splicing, splicing-quantification, splicing-visualization
• Language: Python
• Homepage: http://www.altanalyze.org
• Size: 264 MB
• Stars: 91
• Watchers: 16
• Forks: 29
• Open Issues: 16
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Lists

• awesome_single_cell - ICGS - [Python] - Iterative Clustering and Guide-gene Selection (Olsson et al. Nature 2016). Identify discrete, transitional and mixed-lineage states from diverse single-cell transcriptomics platforms. Integrated FASTQ pseudoalignment /quantification (Kallisto), differential expression, cell-type prediction and optional cell cycle exclusion analyses. Specialized methods for processing BAM and 10X Genomics spares matrix files. Associated single-cell splicing PSI methods (MultIPath-PSI). Apart of the AltAnalyze toolkit along with accompanying visualization methods (e.g., heatmap, t-SNE, SashimiPlots, network graphs). Easy-to-use graphical user and commandline interfaces. (Software packages / RNA-seq)
• awesome-single-cell - ICGS - [Python] - Iterative Clustering and Guide-gene Selection (Olsson et al. Nature 2016). Identify discrete, transitional and mixed-lineage states from diverse single-cell transcriptomics platforms. Integrated FASTQ pseudoalignment /quantification (Kallisto), differential expression, cell-type prediction and optional cell cycle exclusion analyses. Specialized methods for processing BAM and 10X Genomics spares matrix files. Associated single-cell splicing PSI methods (MultIPath-PSI). Apart of the AltAnalyze toolkit along with accompanying visualization methods (e.g., heatmap, t-SNE, SashimiPlots, network graphs). Easy-to-use graphical user and commandline interfaces. (Software packages / RNA-seq)
• awesome-single-cell - ICGS - [Python] - Iterative Clustering and Guide-gene Selection (Olsson et al. Nature 2016). Identify discrete, transitional and mixed-lineage states from diverse single-cell transcriptomics platforms. Integrated FASTQ pseudoalignment /quantification (Kallisto), differential expression, cell-type prediction and optional cell cycle exclusion analyses. Specialized methods for processing BAM and 10X Genomics spares matrix files. Associated single-cell splicing PSI methods (MultIPath-PSI). Apart of the AltAnalyze toolkit along with accompanying visualization methods (e.g., heatmap, t-SNE, SashimiPlots, network graphs). Easy-to-use graphical user and commandline interfaces. (Software packages / RNA-seq)