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GitHub / lqsae / haplotyped-methylome
Reproducibility workflow for Gigante et al., 2018: Using long-read sequencing to detect imprinted DNA methylation
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Fork of scottgigante/haplotyped-methylome
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Forks: 0
Open Issues: 0
License: gpl-3.0
Language:
Repo Size: 4.96 MB
Dependencies:
75
Created: over 4 years ago
Updated: over 4 years ago
Last pushed: about 5 years ago
Last synced: about 1 month ago
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Dependencies
environment.yml
conda
- bioconductor-annotationhub
- bioconductor-biomart
- bioconductor-bsseq
- bioconductor-dss
- bioconductor-edger
- bioconductor-genomicranges
- bioconductor-limma
- bioconductor-rsamtools
- bioconductor-rsubread
- bioconductor-rtracklayer
- biopython
- bismark
- bowtie2
- bwa
- cutadapt
- fastqc
- future
- h5py
- hisat2
- htslib
- nanopolish
- numpy
- ont-fast5-api
- pandoc
- progressbar33
- pysam
- r-broom
- r-cowplot
- r-data.table
- r-devtools
- r-fuzzyjoin
- r-ggextra
- r-glmnet
- r-gridextra
- r-gtable
- r-knitr
- r-mclust
- r-rmarkdown
- r-rpart
- r-tidyverse
- r-viridis
- samtools
- snakemake
- snpsplit
- trim-galore
- AnnotationHub *
- DSS *
- GenomicRanges *
- Rsamtools *
- Rsubread *
- biomaRt *
- bsseq *
- edgeR *
- limma *
- rtracklayer *
r_requirements.txt
pypi