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DegNorm - DegNorm: degradation normalization for RNA-seq data

This package performs degradation normalization in bulk RNA-seq data to improve differential expression analysis accuracy. It provides estimates for each gene within each sample.

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rnaseqnormalizationgeneexpressionalignmentcoveragedifferentialexpressionbatcheffectsoftwaresequencingimmunooncologyqualitycontroldataimportopenblascppopenmp

5.20 score 2 stars 3 scripts 473 downloads

NuPoP - An R package for nucleosome positioning prediction

NuPoP is an R package for Nucleosome Positioning Prediction.This package is built upon a duration hidden Markov model proposed in Xi et al, 2010; Wang et al, 2008. The core of the package was written in Fotran. In addition to the R package, a stand-alone Fortran software tool is also available at https://github.com/jipingw. The Fortran codes have complete functonality as the R package. Note: NuPoP has two separate functions for prediction of nucleosome positioning, one for MNase-map trained models and the other for chemical map-trained models. The latter was implemented for four species including yeast, S.pombe, mouse and human, trained based on our recent publications. We noticed there is another package nuCpos by another group for prediction of nucleosome positioning trained with chemicals. A report to compare recent versions of NuPoP with nuCpos can be found at https://github.com/jiping/NuPoP_doc. Some more information can be found and will be posted at https://github.com/jipingw/NuPoP.

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geneticsvisualizationclassificationnucleosomepositioninghiddenmarkovmodelfortran

5.00 score 546 downloads

DNAcycP2 - DNA Cyclizability Prediction

This package performs prediction of intrinsic cyclizability of of every 50-bp subsequence in a DNA sequence. The input could be a file either in FASTA or text format. The output will be the C-score, the estimated intrinsic cyclizability score for each 50 bp sequences in each entry of the sequence set.

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neuralnetworkstructuralprediction

4.30 score 259 downloads

RiboDiPA - Differential pattern analysis for Ribo-seq data

This package performs differential pattern analysis for Ribo-seq data. It identifies genes with significantly different patterns in the ribosome footprint between two conditions. RiboDiPA contains five major components including bam file processing, P-site mapping, data binning, differential pattern analysis and footprint visualization.

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riboseqgeneexpressiongeneregulationdifferentialexpressionsequencingcoveragealignmentrnaseqimmunooncologyqualitycontroldataimportsoftwarenormalizationcpp

4.18 score 1 scripts 438 downloads

SPECIES - Statistical Package for Species Richness Estimation

Implementation of various methods in estimation of species richness or diversity in Wang (2011)<doi:10.18637/jss.v040.i09>.

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glibc

2.93 score 86 scripts 383 downloads