All Published Workflows

6 workflows that have been reviewed and published

merfishtools-evaluation
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The evaluation of MERFISHtools and the underyling model as published in the corresponding article.
public

public

This Snakemake workflow generates the entire analysis of the forthcoming manuscript "A Bayesian model for single cell transcr...
GO.db org.Hs.eg.db merfishtools biomaRt BiocSklearn GOstats Pandas Snakemake mutoss bitarray common matplotlib networkx numpy scipy seaborn sklearn svgutils
Free
95
bulk-rna-seq-pipeline-se
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Basic RNA-seq analysis for single-end data.
public

public

Pipeline to run basic RNA-seq analysis on single-end data. This is a package of Python and R scripts that enable reading, pro...
GO.db biomaRt PCAtools BiocParallel Bowtie 2 DESeq2 FastQC genefilter GenomicFeatures Glimma limma Pandas pheatmap qvalue Rgraphviz SAMtools Snakemake STAR topGO Trimmomatic vsn cowplot data.table dplyr ggplot2 ggrepel hexbin plyr RColorBrewer reshape2
Free
37
bulk-rna-seq-pipeline-se
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Analyze single-end RNA-Seq data
public

public

Pipeline to run basic RNA-seq analysis on single-end data. This is a package of Python and R scripts that enable reading, pro...
GO.db biomaRt PCAtools BiocParallel Bowtie 2 DeepTools DESeq2 fastp FastQC genefilter GenomicFeatures Glimma limma MultiQC Pandas pheatmap qvalue Rgraphviz SAMtools Snakemake STAR topGO vsn cowplot data.table dplyr ggplot2 ggrepel hexbin plyr RColorBrewer reshape2 stringr
Free
41
cfrna-seq-pipeline-ngo-manuscript-2019
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This pipeline contains the data processing steps used for Thuy Ngo's 2019 cell-free RNA manuscript
public

public

Pipeline to process raw fastq files for Thuy Ngo's manuscript: "Plasma cell-free RNA profiling enables pan-cancer detection a...
GO.db biomaRt PCAtools BiocParallel Bowtie 2 DESeq2 FastQC genefilter GenomicFeatures Glimma HTSeq htseqcount limma Pandas pheatmap qvalue Rgraphviz SAMtools sickle Snakemake STAR topGO vsn cowplot data.table dplyr ggplot2 ggrepel hexbin plyr RColorBrewer reshape2
Free
49
rna-seq-pop
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RNA-Seq-Pop: Analysis Workflow for Illumina Paired-End RNA Sequencing Data
public

public

This snakemake workflow performs various analyses of illumina paired-end RNA-Sequencing data: Quality control of fastq re...
GO.db JSON gatk snakemake-wrapper-utils EnhancedVolcano BCFtools Cutadapt DESeq2 FastQC fgsea FreeBayes gage GLUE GSEA HISAT2 kallisto kissDE mosdepth MultiQC octopus Pandas pheatmap QualiMap Quant rtracklayer SAMBLASTER SAMtools sleuth Snakemake snpEff SnpSift Vcflib data.table dplyr ggplot2 ggrepel jsonlite openxlsx RColorBrewer tidyverse adjustText matplotlib matplotlib-venn numpy pop-tools scipy zarr RNA-Seq
Free
81
rnaseq-workflow
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Differential Gene Expression using RNA-Seq
public

public

RNAseq is becoming the one of the most prominent methods for measuring celluar responses. Not only does RNAseq have the abili...
GO.db org.Hs.eg.db org.Mm.eg.db Differential gene expression profiling biomaRt PCAtools clusterProfiler DESeq2 DOSE FastQC FeatureCounts gage genefilter MultiQC pathview pheatmap ReactomePA SortMeRNA STAR topGO dplyr ggplot2 ggsci knitr RColorBrewer Trim_Galore RNA-Seq
Free
44