jrboyd Goto Github PK

badrito_sim

simulation of hands for badrito game

diff_marks

analysis of differential marks in ChIP-seq data

dthic

A HiC analysis package (requires binned values) that makes heavy use of data.table

exptsne

TSNE augmented analysis of large sequencing datasets

features_at_tad_boundary_enrichment

compares interval features to TAD boundaries

hic_histone_genes

analysis using sushi package of dave's hicr results

image_analysis

R based image analysis

jrb_r_scripts

jrboyd's frequently used R scripts

jrb_r_scripts_public

general use scripts more fit for public consumption

jrb_shinyapps

jrboyd's shiny apps

monocle_helpr

helps keep monocle results organized and reproducible

paper2_v2

pipelines for bivalency paper

paper3_v3

drug treatment epigenetic and expression response

paper_uniq2gsea

ngs plots and membership heatmaps relating uniquely to gsea

paper_v5

figures 2, 5, and 6

paper_v6

completed figure generation pipeline for K4 paper

pchic_3t3l1

peakrefine

refining peaks using metrics derived from aligned read strand information

pycistarget

pycistarget is a python module to perform motif enrichment analysis in sets of regions with different tools and identify high confidence TF cistromes.

qc_framework

regulation_and_correlation

revigo_test

scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.

scrape_geo

functions to scrape GEO for SRR and fetch fastq files

scrna_dk

scripts for anlaysis of Dimitry's scRNAseq of microglial cells

seqqc

Utilizes seqsetvis to prodce qc plots. Namely, peak overlap with signal, SCC, and FRIP.

seqsetvis

Allows general set comparisons with a focus on sets of genomic locations (ChIP-seq peaks primarily). The includes standard visualizations such as venn and euler diagrams but more powerfully of genomic signal pulled from bigwig files.

seqtsne

seqtsne

sf_examples

quick projects and examples for SF and MM

shiny_auto_ucsc

shiny app and underlying code for viewing annotation, RNAseq, ChIPseq and segmentation results.