JosephLalli
MD/PhD Graduate Student at the University of Wisconsin-Madison. I enjoy thinking about how ACGTs change, and what those changes do.
Werling LabMadison, WI
Pinned Repositories
pangenie
Pangenome-based genome inference
1KGP_T2T_pangenie
bonito
Bonito - A PyTorch Basecaller for Oxford Nanopore Reads
fishpond
Differential transcript and gene expression, as well as helper functions for working with Salmon, alevin, and alevin-fry data
g2gtools
Personal diploid genome creation and coordinate conversion
leafcutter
Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard
modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
phasing_T2T
Repository for code to produce phased 1000 Genomes Project haplotypes called against the CHM13v2 T2T reference genome.
PiMaker
Tool to calculate nucleotide diversity statistics in large pooled population datasets
statannotations
add statistical annotations (pvalue significance) on existing boxplot/barplot generated by seaborn
JosephLalli's Repositories
JosephLalli/phasing_T2T
Repository for code to produce phased 1000 Genomes Project haplotypes called against the CHM13v2 T2T reference genome.
JosephLalli/PiMaker
Tool to calculate nucleotide diversity statistics in large pooled population datasets
JosephLalli/1KGP_T2T_pangenie
JosephLalli/bonito
Bonito - A PyTorch Basecaller for Oxford Nanopore Reads
JosephLalli/fishpond
Differential transcript and gene expression, as well as helper functions for working with Salmon, alevin, and alevin-fry data
JosephLalli/g2gtools
Personal diploid genome creation and coordinate conversion
JosephLalli/leafcutter
Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard
JosephLalli/modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
JosephLalli/statannotations
add statistical annotations (pvalue significance) on existing boxplot/barplot generated by seaborn
JosephLalli/nextflow
A DSL for data-driven computational pipelines
JosephLalli/pangenie
Incorporating pre/post variant filtering when aligning to reference pangenomes
JosephLalli/personalized_rnaseq
JosephLalli/qtlmap
Portable eQTL analysis and statistical fine mapping workflow used by the eQTL Catalogue
JosephLalli/rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control. Includes ngscheckmate.
JosephLalli/sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
JosephLalli/statannot
add statistical annotations (pvalue significance) on an existing boxplot generated by seaborn boxplot
JosephLalli/taiyaki
Training models for basecalling Oxford Nanopore reads
JosephLalli/tensorqtl_susie_suff_stats
Ultrafast GPU-based QTL mapper
JosephLalli/VCFclass