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awesome-single-cell - List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc

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List of software packages (and the people developing these methods) for single-cell data analysis, including RNA-seq, ATAC-seq, etc. Contributions welcome... Gender bias at conferences is a well known problem (http://www.sciencemag.org/careers/2015/07/countering-gender-bias-conferences). Creating a list of potential speakers can help mitigate this bias and a community of people developing and maintaining helps to further diversify this list beyond smaller networks.

altanalyze - AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses

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AltAnalyze is an extremely user-friendly and open-source analysis tool that can be used for a broad range of genomics analyses. These analyses include the direct processing of raw RNASeq or microarray data files, advanced methods for single-cell population discovery, differential expression analyses, analysis of alternative splicing/promoter/polyadenylation and advanced isoform function prediction analysis (protein, domain and microRNA targeting). Multiple advanced visualization tools and à la carte analysis methods are supported in AltAnalyze (e.g., network, pathway, splicing graph). AltAnalyze is compatible with various data inputs for RNASeq data (FASTQ, BAM, BED), microarray platforms (Gene 1.0, Exon 1.0, junction and 3' arrays). This software requires no advanced knowledge of bioinformatics programs or scripting or advanced computer hardware. User friendly videos, online tutorials and blog posts are also available. AltAnalyze documentation, stand-alone archives are provided at sourceforge as well as at github. For questions not addressed here, please contact us.