caixu0518
I am a postdoctoral researcher at the Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, focusing on genomic analysis of Brassica.
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science12 Zhongguancun Nandajie, Haidian, Beijing 100081, China
Pinned Repositories
ITIPs
Identification of transposable element insertion polymorphisms (TIPs) based on a pan-genome and large-scale resequencing data
MisjoinDetect
An automated misjoins correction pipeline (named MisjoinDetect) based on Hi-C data
MicroSynPlot
Micro-syntenic plot of two and more genomic segments
MyPerlScripts
my perl scripts
annotation_pl
Scripts used for Brassica rapa gene model prediction
ClustersPloter
visualize genome features cluster(gene arrow map or other features), add synteny among genome fragments or add crosslink among features, add short(PE/MP)/long reads(pacbio or nanopore) mapping or snpindel in vcf(not support complex sv yet), support all CIGAR of sam alignment, directly modify almost all features in web browser by click the feature, fragments genome view
CtgRef-CNV
CNV calling method based on assembly and read depth of NGS data
dCNS
conserved non-coding sequence
DensityMap
DensityMap is perl tool for the visualization of features density along chromosomes
EDTA
Extensive de-novo TE Annotator
caixu0518's Repositories
caixu0518/annotation_pl
Scripts used for Brassica rapa gene model prediction
caixu0518/ITIPs
Identification of transposable element insertion polymorphisms (TIPs) based on a pan-genome and large-scale resequencing data
caixu0518/Populus-Genomic-Consequences-of-Hybridization
caixu0518/genomeAlignment
Compare different genome alignment tools using a wide range of genomes with different complexities.
caixu0518/dCNS
conserved non-coding sequence
caixu0518/TEMP2
Algorithm to detect germline and de novo transposon insertions
caixu0518/MicroSynPlot
Micro-syntenic plot of two and more genomic segments
caixu0518/MyPerlScripts
my perl scripts
caixu0518/CtgRef-CNV
CNV calling method based on assembly and read depth of NGS data
caixu0518/RelocaTE2
RelocaTE2
caixu0518/MisjoinDetect
An automated misjoins correction pipeline (named MisjoinDetect) based on Hi-C data
caixu0518/GSAlign
GSAlign: an ultra-fast sequence alignment algorithm for intra-species genome comparison
caixu0518/syri
Synteny and Rearrangement Identifier
caixu0518/sv-cnv-studies
caixu0518/tank
《蓝眼云盘》(Eyeblue Cloud Disk)
caixu0518/PhyLTR
Phylogenetic Analysis of Long Terminal Repeat Retrotransposons
caixu0518/seqtk
Toolkit for processing sequences in FASTA/Q formats
caixu0518/Scripts_for_GB
The code used in the manuscript titled "Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants".
caixu0518/link_3D_dna_scfs_to_chromosomes
caixu0518/EDTA
Extensive de-novo TE Annotator
caixu0518/ClustersPloter
visualize genome features cluster(gene arrow map or other features), add synteny among genome fragments or add crosslink among features, add short(PE/MP)/long reads(pacbio or nanopore) mapping or snpindel in vcf(not support complex sv yet), support all CIGAR of sam alignment, directly modify almost all features in web browser by click the feature, fragments genome view
caixu0518/Split_genes
caixu0518/JustOrthologs
caixu0518/PopLDdecay
PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
caixu0518/DensityMap
DensityMap is perl tool for the visualization of features density along chromosomes
caixu0518/PseudogenePipeline
caixu0518/jcvi
Python utility libraries on genome assembly, annotation and comparative genomics
caixu0518/Scripts