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centrifuger Public
Taxonomic classifier for sequencing reads (bulk and single-cell data, short and long read) using FM-index with run-block compressed BWT.
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pvalannot Public
Add p-value annotation to the plot
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ReadFormatter Public
The C++ class for extracting and concatenating segments from sequencing read
C++ MIT License UpdatedJan 20, 2026 -
Lighter Public
Fast and memory-efficient sequencing error corrector
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Rcorrector Public
Error correction for Illumina RNA-seq reads
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scSnpMarker Public
Scripts for identifying informative SNPs to distinguish cells in group 0 and 1, and then use them to classify gruop -1 (unkown) cells.
Python MIT License UpdatedDec 23, 2025 -
T1K Public
T1K is a versatile methods to genotype highly polymorphic genes (e.g. KIR, HLA) with bulk or single-cell RNA-seq, WGS or WES data.
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pickseq_analysis Public
The analysis for the SMART-seq data from the LiP-seq (previously called pickseq) manuscript
Jupyter Notebook UpdatedMar 25, 2025 -
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bioconda-recipes Public
Forked from bioconda/bioconda-recipesConda recipes for the bioconda channel.
Shell MIT License UpdatedJan 17, 2025 -
hisat2 Public
Forked from DaehwanKimLab/hisat2Graph-based alignment (Hierarchical Graph FM index)
C++ GNU General Public License v3.0 UpdatedOct 21, 2024 -
MSAplot Public
Plot multiple sequence alignment (MSA)
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T1K_manuscript_evaluation Public
The scripts used in the T1K manuscript
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chromap Public
Forked from haowenz/chromapFast alignment and preprocessing of chromatin profiles
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csvjoin Public
A python script that selects a key and columns from csv B and append that to csv file A . Require pandas.
Python UpdatedJan 19, 2024 -
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heatmapannot Public
Add color heatmap to seaborn heatmaps
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hlaproject Public
Forked from ydottie/hlaprojectRigorous benchmarking of HLA callers for RNA seq data
Jupyter Notebook MIT License UpdatedNov 1, 2023 -
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liulab-dfci.github.io Public
Forked from liulab-dfci/liulab-dfci.github.ioKnow more about Shirley Liu lab at
HTML Other UpdatedOct 15, 2022 -
DeepCAT Public
Forked from s175573/DeepCATDeep Learning Method to Identify Cancer Associated TCRs - modified to output score for each CDR3
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arcasHLA Public
Forked from RabadanLab/arcasHLAFast and accurate in silico inference of HLA genotypes from RNA-seq
Python GNU General Public License v3.0 UpdatedJul 9, 2021 -
CLASS Public
Constraint-based Local Assembly and Selection of Splice variants
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iSMART Public
Forked from s175573/iSMARTHighly specific clustering of T cell receptor CDR3s
Python UpdatedFeb 20, 2020 -
mixcr-rna-seq-paper Public
Forked from milaboratory/mixcr-rna-seq-paperIn silico data and tests
Jupyter Notebook UpdatedJul 17, 2018 -
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