Qionghou Li's repositories
paml-yn00-run-pipeline
A personal pipeline to calculate Ka,Ks and Ka/Ks using PAML-yn00 with YN method
DeepLearning-500-questions
深度学习500问，以问答形式对常用的概率知识、线性代数、机器学习、深度学习、计算机视觉等热点问题进行阐述，以帮助自己及有需要的读者。 全书分为17个章节，20多万字。由于水平有限，书中不妥之处恳请广大读者批评指正。 未完待续............ 如有意合作，联系scutjy2015@163.com 版权所有，违权必究 Tan 2018.06
Pear_Haplotype_Genome
Codes for pear haplotype genome and pangenome graph construction
AED-distribution-plot
plot the cumulative AED distribution controlling the quality of annotation for the final gene predictions
AMPRIL-genomes
scripts for the project of seven thaliana genomes assembly
cDNA_Cupcake
Miscellaneous collection of Python and R scripts for processing Iso-Seq data
cheatsheets
RStudio Cheat Sheets
clust
Automatic and optimised consensus clustering of one or more heterogeneous datasets
DupGen_finder
A pipeline used to identify different modes of duplicated gene pairs
EDTA
Extensive de-novo TE Annotator
GCE
GCE (genomic charactor estimator) is a bayes model based method to estimate the genome size, genomic repeat content and the heterozygsis rate of the sequencing sample. The estimated result can be used to design the sequencing strategy.
Genome-data-of-Hanfu-apple
FASTA files of chromosomes and genes, gff files for gene models.
hickit
TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
IsoSeq
IsoSeq3 - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
LTR_retriever
LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
Maize_NC358
The repository for codes developed to generated the Maize NC358 assemblies and analyses.
oneliners
Useful bash one-liners for bioinformatics.
pyGenomeTracks
python module to plot beautiful and highly customizable genome browser tracks
Scripts_for_GB
The code used in the manuscript titled "Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants".
syri
Synteny and Rearrangement Identifier
tmhmm.py
A transmembrane helix finder in Python 3.
tutorials
Tutorials on phylogenetic and phylogenomic inference
vcf2phylip
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
watchdog_for_jobs
watch a job is running or finish then send e-mail