DESeq2 - Differential gene expression analysis based on the negative binomial distribution
Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.
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sequencingrnaseqchipseqgeneexpressiontranscriptionnormalizationdifferentialexpressionbayesianregressionprincipalcomponentclusteringimmunooncologyopenblascpp
17.09 score 488 stars 144 dependents 38k scripts 72k downloadstximport - Import and summarize transcript-level estimates for transcript- and gene-level analysis
Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Average transcript length, weighted by sample-specific transcript abundance estimates, is provided as a matrix which can be used as an offset for different expression of gene-level counts.
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dataimportpreprocessingrnaseqtranscriptomicstranscriptiongeneexpressionimmunooncologybioconductordeseq2
13.42 score 146 stars 13 dependents 5.3k scripts 8.6k downloadstximeta - Transcript Quantification Import with Automatic Metadata
Transcript quantification import from Salmon and other quantifiers with automatic attachment of transcript ranges and release information, and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility.
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annotationgenomeannotationdataimportpreprocessingrnaseqlongreadsinglecelltranscriptomicstranscriptiongeneexpressionfunctionalgenomicsreproducibleresearchreportwritingimmunooncology
11.80 score 72 stars 2 dependents 635 scripts 3.8k downloadsfishpond - Fishpond: downstream methods and tools for expression data
Fishpond contains methods for differential transcript and gene expression analysis of RNA-seq data using inferential replicates for uncertainty of abundance quantification, as generated by Gibbs sampling or bootstrap sampling. Also the package contains a number of utilities for working with Salmon and Alevin quantification files.
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sequencingrnaseqgeneexpressiontranscriptionnormalizationregressionmultiplecomparisonbatcheffectvisualizationdifferentialexpressiondifferentialsplicingalternativesplicingsinglecellbioconductorgene-expressiongenomicssalmonscrnaseqstatisticstranscriptomics
8.06 score 33 stars 292 scripts 1.5k downloadssplicelogic - splicelogic: differential transcripts to splice events
Translate differential transcript usage results into discrete splice events.
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alternativesplicingdifferentialsplicingtranscriptomicsrnaseqlongreadannotationfunctionalgenomicsdtusplicing
6.18 score 4 stars 7 scripts 296 downloadsrnaseqGene - RNA-seq workflow: gene-level exploratory analysis and differential expression
Here we walk through an end-to-end gene-level RNA-seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were aligned to the reference genome, and prepare a count matrix which tallies the number of RNA-seq reads/fragments within each gene for each sample. We will perform exploratory data analysis (EDA) for quality assessment and to explore the relationship between samples, perform differential gene expression analysis, and visually explore the results.
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workflowgeneexpressionworkflowimmunooncologyworkflow
5.90 score 81 stars 31 scriptsrnaseqDTU - RNA-seq workflow for differential transcript usage following Salmon quantification
RNA-seq workflow for differential transcript usage (DTU) following Salmon quantification. This workflow uses Bioconductor packages tximport, DRIMSeq, and DEXSeq to perform a DTU analysis on simulated data. It also shows how to use stageR to perform two-stage testing of DTU, a statistical framework to screen at the gene level and then confirm which transcripts within the significant genes show evidence of DTU.
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workflowgeneexpressionworkflowimmunooncologyworkflow
5.51 score 23 stars 10 scripts