What is AltAnalyze?

AltAnalyze is an extremely user-friendly and open-source analysis toolkit 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.

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1 Introduction

2 Running AltAnalyze

3 Algorithms

4 Using R with AltAnalyze

5 Software Infrastructure

6 Building AltAnalyze Annotation Files

7 Evaluation of AltAnalyze Predictions

8 Analysis of AltAnalyze Results DomainGraph