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IMOM - A pipeline for interacting with, processing, and analyzing multi-OM datasets in phylogenetic and evolutionary context

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10 Commits
What I Used for Mus + Aco
What I Used for Mus + Aco
 
 
10_run_prepDE.py3.sh
10_run_prepDE.py3.sh
 
 
11.1_DESeq2_markdown.rmd
11.1_DESeq2_markdown.rmd
 
 
11_DESeq2.r
11_DESeq2.r
 
 
14_figures.py
14_figures.py
 
 
2.2_unzip_fastq.sh
2.2_unzip_fastq.sh
 
 
3.1_hisat2_align_paired.sh
3.1_hisat2_align_paired.sh
 
 
4_samtools.sh
4_samtools.sh
 
 
5_stringtie.sh
5_stringtie.sh
 
 
6_stringtie_merge.sh
6_stringtie_merge.sh
 
 
7_gffcompare.sh
7_gffcompare.sh
 
 
8_stringtie_transcript_abundance.sh
8_stringtie_transcript_abundance.sh
 
 
9_download_prepDE.py3.sh
9_download_prepDE.py3.sh
 
 
Acomys_Mus_Orthology (3).xlsx
Acomys_Mus_Orthology (3).xlsx
 
 
BetasToMValues.r
BetasToMValues.r
 
 
BetastoM.r
BetastoM.r
 
 
Density Delta Mus.png
Density Delta Mus.png
 
 
DensityDeltaAco.png
DensityDeltaAco.png
 
 
README.md
README.md
 
 
Visualize Distribution.R
Visualize Distribution.R
 
 
calc_pvalue.r
calc_pvalue.r
 
 
consensus_sequence.txt
consensus_sequence.txt
 
 
delta.r
delta.r
 
 
extract_density_curve.R
extract_density_curve.R
 
 
foldchange.r
foldchange.r
 
 
heatmap2.r
heatmap2.r
 
 
pvalue.r
pvalue.r
 
 
sample_sheet.tsv
sample_sheet.tsv
 
 
search_consensus_gpt.py
search_consensus_gpt.py
 
 
search_local.py
search_local.py
 
 
sesame - betas to m.r
sesame - betas to m.r
 
 
sesameAnno.r
sesameAnno.r
 
 
sesame_preprocessing.r
sesame_preprocessing.r
 
 
stats.r
stats.r
 
 
volcanoplot.r
volcanoplot.r
 
 
welchs.r
welchs.r
 
 

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Integrative Multi-OM

- IMOM -

Illumina Methyl40 bead-chip, Clock Consortium Infinium v2.0

DNB Double Stranded Eukaryotic RNAsequencing - polyA

SESAME

Statistical Analysis -

  • DMR, DML
  • Linear regression penalized reinforcement modeling (?)

Aligment of CTCF binding site motifs to novel genome

  • HiC
  • Integration with existing orthologous transcription factor datasets
  • ChipSeq

RNAseq alignment

  • Modeling

Epigenetic Clock -

  • SpinyMouse
  • SpinyMouse_Mus

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IMOM - A pipeline for interacting with, processing, and analyzing multi-OM datasets in phylogenetic and evolutionary context

Topics

bioinformatics evolution methylation rnaseq phylogeny illumina-sequencing illumina-bead-chip rnaseq-analysis

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