isaacvock Goto Github PK

alpine

Modeling and correcting fragment sequence bias for RNA-seq

annotationcleaner

Cleaning transcriptome annotations with ab initio assemblers

baknpy

Python rewrite of bakR (for self-educational purposes)

costseq

ezbakr

Significantly expanding the functionality and flexibility of bakR

factr2

Functional Annotation of Custom Transcriptomes v2

fastq2bakr

Extension of rna-seq-star-deseq2 Snakemake workflow to process NR-seq data for bakR

fastq2ezbakr

Significantly improved bam2bakR implementation

featurecounts_repex

Reproducible example for featureCounts bug posted to Bioconductor support

flatstacks

Flattening annotation for bakR

fq2bakr

Snakemake implementation of Simon lab TimeLapse pipeline

hdprobe

R package for performing differential mutation analysis

isaacvock.github.io

jcc

R package to calculate junction coverage compatibility (JCC) scores

nrsim

NR-seq (TimeLapse-seq, SLAM-seq, TUC-seq, etc.) fastq simulation pipeline

pipelinedocs

One-stop-shop for documentation of my Snakemake pipelines

proseq_etal

PRO-seq + ChIP-seq pipeline, with potential NET-seq/ATAC-seq/etc. extensions

pulse_chase

Script for analyzing pulse chase data with bakR

pythoninstallation

Helping MB&B 121L students install Python

readthedocs_tutorial

scrnaseq_cuzynot

scRNAseq Snakemake pipeline for the sake of self-education

slamdunk

Streamlining SLAM-seq analysis with ultra-high sensitivity

stantest

Repository to test if configure files are necessary for installation from Github

statistical_intuition_book

Book to accompany "Statistical Intuition for Modern Biologists"

statistical_modeling_intro

Materials I developed for an intro to statistical modeling/simulations workshop

test_workflow_2

Toy Snakemake workflow to test modularization syntax

the_aligner

Align almost any kind of RNA-seq data

tl-snakemake

Snakemake implementation of TimeLapse pipeline developed by Simon lab

yale_profile

Snakemake profile template for Yale HPC