shulp2211

Pinned Repositories

abstar
VDJ assignment and antibody sequence annotation. Scalable from a single sequence to billions of sequences.
Language:Python1 1 00
AnnotationPipeline-EVM_based-DClab
Cantù Lab @ UC Davis - Annotation pipeline - EVM based
Language:Python1 1 00
Awesome-Bioinformatics
A curated list of awesome Bioinformatics libraries and software.
2 1 00
BAMreport
Report on a BAM file
Language:C3 1 01
bioinformatics
this is a hub for bioinformatics
1 1 00
chip-seq-pipeline2
ENCODE ChIP-seq pipeline
Language:Python10
Chromatin_Analysis_2020_cell
Source codes and example scripts for chromatin tracing projects in Zhuang lab
Language:Jupyter Notebook1 1 00
cov2tree
Cov2Tree website, based on Taxodium
Language:HTML1 0 00
covtobed
⛰ covtobed | Convert the coverage track from a BAM file into a BED file
Language:C++1 1 00
google-research
Google Research
Language:Jupyter Notebook1 0 00

shulp2211's Repositories

shulp2211/Awesome-Bioinformatics
A curated list of awesome Bioinformatics libraries and software.
2 1 00
shulp2211/AnnotationPipeline-EVM_based-DClab
Cantù Lab @ UC Davis - Annotation pipeline - EVM based
Language:Python1 1 00
shulp2211/cov2tree
Cov2Tree website, based on Taxodium
Language:HTML1 0 00
shulp2211/covtobed
⛰ covtobed | Convert the coverage track from a BAM file into a BED file
Language:C++1 1 00
shulp2211/google-research
Google Research
Language:Jupyter Notebook1 0 00
shulp2211/HaploSync
Tools for haplotype-wise reconstruction of pseudomolecules
Language:Python1 1 0
shulp2211/hts-specs
Specifications of SAM/BAM and related high-throughput sequencing file formats
Language:TeX1 1 0
shulp2211/htseq
HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
Language:Python1 1 0
shulp2211/kent
UCSC Genome Browser source tree. Stable branch: "beta".
Language:C1 0 0
shulp2211/ldsc
LD Score Regression (LDSC)
Language:Python1 0 0
shulp2211/ML-YouTube-Courses
A repository to index and organize the latest machine learning courses found on YouTube.
1 1 0
shulp2211/models-1
Model zoo for genomics
Language:Python1 0 0
shulp2211/Monopogen
Single Cell Population Genetics and Association Analysis Tool
Language:Python1 0 0
shulp2211/mosdepth
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
Language:Nim1 0 0
shulp2211/neuromaps
A toolbox for comparing brain maps
Language:Python1 0 0
shulp2211/paraphase
HiFi-based SMN1 and SMN2 caller
Language:Python1 0 0
shulp2211/pb-16S-nf
Nextflow pipeline to analyze PacBio HiFi full-length 16S data
Language:Nextflow1 0 0
shulp2211/pb-human-wgs-workflow-snakemake
Workflow for the comprehensive detection and prioritization of variants in human genomes with PacBio HiFi reads
Language:Python1 0 0
shulp2211/picard
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Language:Java1 1 0
shulp2211/PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
Language:Python1 0 0
shulp2211/PyWGCNA
PyWGCNA is a Python package designed to do Weighted Gene Correlation Network analysis (WGCNA)
Language:Jupyter Notebook1 0 0
shulp2211/rna-tools
🔧rna-tools: a toolbox to analyze sequences, structures and simulations of RNA (and more) docs @ http://rna-tools.rtfd.io web @ http://rna-tools.online
Language:Jupyter Notebook1 1 0
shulp2211/scEvoNet
scEvoNet is a tool for generation a cell type - gene program network between species or different time points in the same organism.
Language:Jupyter Notebook1 0 0
shulp2211/scRNA-seq_notes
A list of scRNA-seq analysis tools
Language:R1 0 0
shulp2211/simCAS
simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data
Language:Jupyter Notebook1 0 0
shulp2211/single_cell_pipeline
Single Cell Analysis Automated Workflow
Language:Python1 0 0
shulp2211/STAR-Fusion
STAR-Fusion codebase
Language:Perl1 1 0
shulp2211/taxonium
Explore very large trees in the browser
Language:JavaScript1 0 0
shulp2211/usher
Ultrafast Sample Placement on Existing Trees
Language:C++1 0 0
shulp2211/yahs
Yet another Hi-C scaffolding tool
1