AltAnalyze statistics

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Citations per year

Number of citations per year for the bioinformatics software tool AltAnalyze
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Tool usage distribution map

This map represents all the scientific publications referring to AltAnalyze per scientific context
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Associated diseases

This word cloud represents AltAnalyze usage per disease context
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Popular tool citations

chevron_left Clustering Bioinformatics workflows Novel transcript quantification Alternative splicing events identification Gene expression clustering Batch effect removal Normalization Known transcript quantification Transcript quantification Marker gene detection Classification Dimensionality reduction Bioinformatics workflows Differential expression detection Cell cycle Alternative splicing detection Gene filtering Alternative splicing detection Transcriptome annotation Gene network prediction Gene set prediction Differential usage Exon skipping detection Batch effect correction Probe filtering chevron_right
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Protocols

AltAnalyze specifications

Information


Unique identifier OMICS_02250
Name AltAnalyze
Software type Pipeline/Workflow
Interface Command line interface, Graphical user interface
Restrictions to use None
Input format FASTQ, BAM, BED, CEL
Output format PDF, PNG
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 2.1.0
Stability Stable
Maintained Yes

Versioning


No version available

Additional information


https://github.com/nsalomonis/altanalyze https://altanalyze.readthedocs.io/en/latest/

Publications for AltAnalyze

AltAnalyze citations

 (49)
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Gene Expression of Pneumocystis murina after Treatment with Anidulafungin Results in Strong Signals for Sexual Reproduction, Cell Wall Integrity, and Cell Cycle Arrest, Indicating a Requirement for Ascus Formation for Proliferation

2018
Antimicrob Agents Chemother
PMCID: 5923105
PMID: 29463544
DOI: 10.1128/AAC.02513-17
call_split See protocol

[…] Raw shotgun reads were trimmed from both ends by 3 nucleotides to remove adaptor and low-quality sequences, resulting in 45-bp reads. RNA-seq data for the mouse and Pneumocystis were analyzed using AltAnalyze (), which employs Kallisto for ultrafast mapping of transcripts (). Gene expression was computed as log2-transformed transcripts per million (TPM). Significance of differential expression w […]

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The Effects of PPAR Stimulation on Cardiac Metabolic Pathways in Barth Syndrome Mice

2018
Front Pharmacol
PMCID: 5904206
PMID: 29695963
DOI: 10.3389/fphar.2018.00318
call_split See protocol

[…] na HiSeq platform, with 40 million reads. RNA-sequencing results were deposited at the Sequence Read Archive at NCBI (Accession ID SRP132110). For bioinformatics analysis, BAM files were submitted to AltAnalyze software package (v.2.1.0). […]

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Alternative transcription of a shorter, non anti angiogenic thrombospondin 2 variant in cancer associated blood vessels

2018
Oncogene
PMCID: 5945577
PMID: 29467494
DOI: 10.1038/s41388-018-0129-z
call_split See protocol

[…] particular exon in a transcript. SI values of 1 and −1 were used as arbitrary thresholds. We used this SI in an analysis of variance (ANOVA) model named MIDAS [], using Genespring Gx 12 (Agilent) and Altanalyze [] to test the null hypothesis that no alternative splicing occurs for a particular exon. For the sake of clarity, SI when used in the MIDAS ANOVA model is called MIDAS score. Exons with a […]

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Different Non Saccharomyces Yeast Species Stimulate Nutrient Consumption in S. cerevisiae Mixed Cultures

2017
Front Microbiol
PMCID: 5671574
PMID: 29163412
DOI: 10.3389/fmicb.2017.02121
call_split See protocol

[…] on values showing higher adjusted p-values were never taken into consideration for data analysis or discussion, independently of the associated LogFC.Principal component analysis (PCA) was done using AltAnalyze software (2.1.0) (). AltAnalyze was feeded with the normalized RNAseq data transcripts per million (TPM). The remaining statistical analyses were done using STATA-SE. Venn diagram was done […]

library_books

Alignment of Mitotic Chromosomes in Human Cells Involves SR Like Splicing Factors Btf and TRAP150

2017
Int J Mol Sci
PMCID: 5618605
PMID: 28895891
DOI: 10.3390/ijms18091956

[…] ach sample was hybridized and subjected to automated washing, staining, and scanning on the Fluidics Station 450 (Affymetrix) following fluidics protocol FS450-0001. Array results were analyzed using AltAnalyze [] for differential gene expression in control versus Btf- or TRAP150-depleted samples as described in Ref. []. The primary data have been deposited in the NCBI GEO database under the acces […]

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Meta analysis of transcriptomic datasets identifies genes enriched in the mammalian circadian pacemaker

2017
Nucleic Acids Res
PMCID: 5737434
PMID: 28973476
DOI: 10.1093/nar/gkx714
call_split See protocol

[…] Microarray data were processed as series of comparisons for each microarray platform, or RNA-Seq data. CEL files were imported in to AltAnalyze (version 2.9.0.2) and processed via integration with Affymetrix power-tools (APT), using the Robust Multi-array Averaging (RMA-sketch) algorithm. Following removal of probes known to cross- […]


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AltAnalyze institution(s)
Max Planck Institute for Informatics, Saarbrücken, Germany

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