AltAnalyze protocols

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Popular tool citations

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

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Additional information


https://github.com/nsalomonis/altanalyze

Publications for AltAnalyze

AltAnalyze in pipelines

 (9)
2017
PMCID: 5367350
PMID: 28098904
DOI: 10.3892/mmr.2017.6123

[…] icc samples compared with healthy liver tissues were identified via the limma package, following data preprocessing. genes that exhibited alternative splicing (as) in icc samples were identified via altanalyze software. functional enrichment analysis of degs was performed using the database for annotation, visualization and integrated analysis. target genes of dems were identified using […]

2017
PMCID: 5737434
PMID: 28973476
DOI: 10.1093/nar/gkx714

[…] aligned to the mm10 genome using tophat2 (). when unpublished, library strand direction was confirmed with manual inspection in the integrative genomics viewer (). junction bed files were sent to altanalyze for downstream gene annotation, counting and differential expression analysis (). per-identifier es values were then calculated as described above., all data were indexed against mgi gene […]

2016
PMCID: 4725928
PMID: 26763932
DOI: 10.1038/srep19251

[…] for cross-hybridisation and those with very large gene-level normalised intensities. software parameters were set to default values, except for the splice index cutoff, which was set to 0.5. altanalyze is an open-source software utilising the firma algorithm which is another method for detection of alternative splicing. software parameters were set to default values, except […]

2016
PMCID: 4931246
PMID: 27350239
DOI: 10.1038/ncomms12060

[…] tophat v2.0.9 (ref. ) using default parameters against the whole genome assembly of human (grch37) with the corresponding gtf annotation. as events and corresponding expression were detected using altanalyze with default parameters for rna-seq reads. corresponding long poly(a)-/rrna-rna data were processed by ciri-as as mentioned above. the detection results of both ciri-as and altanalyze […]

2016
PMCID: 4961522
PMID: 27294509
DOI: 10.1038/nn.4322

[…] (go) analysis was performed using the database for annotation, visualization and integrated discovery (david; http://david.abcc.ncifcrf.gov). the heatmap was generated based on log2 [fpkm] by altanalyze , with normalization of rows relative to row mean., chip assays were performed as described with minor modifications ,. briefly, purified rat scs grown in proliferation and differentiation […]


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AltAnalyze in publications

 (65)
PMCID: 5923105
PMID: 29463544
DOI: 10.1128/AAC.02513-17

[…] 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 […]

PMCID: 5904206
PMID: 29695963
DOI: 10.3389/fphar.2018.00318

[…] 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)., rna-seq reads were aligned to the mouse reference sequence (grcm38) using tophat, and transcripts were assembled with cufflinks package (). differential […]

PMCID: 5945577
PMID: 29467494
DOI: 10.1038/s41388-018-0129-z

[…] 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 […]

PMCID: 5671574
PMID: 29163412
DOI: 10.3389/fmicb.2017.02121

[…] 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 […]

PMCID: 5799810
PMID: 29086765
DOI: 10.1038/cr.2017.135

[…] was conducted using morpheus (broad institute, boston, ma, usa) and ranked by t-test statistics. for gene network and cdt analysis, expression levels were normalized with the rms method. the altanalyze pipeline was used to perform the go-elite analysis with 1.5-fold expression and 0.1 fischer exact test as threshold parameters. cdt visualization was composed using tableau 9.0 (tableau, […]


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

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