Pinned Repositories
biogo
biogo is a bioinformatics library for Go
csvtk
A cross-platform, efficient and practical CSV/TSV toolkit in Golang
ensembl-compara
The Ensembl Compara Perl API and SQL schema
hammerpede
A package for training strand-specific profile HMMs for primer sets from real Nanopore data
isONclust2
A tool for de novo clustering of long transcriptomic reads
phylosim
An R package for the Monte Carlo simulation of sequence evolution
rlsim
A package for simulating RNA-seq library preparation with parameter estimation
simcopy
An R package simulating the evolution of copy number profiles along a tree
spliced_bam2gff
thist
A go package for generating online histograms and plotting them in the terminal and PDFs
botond-sipos's Repositories
botond-sipos/csvtk
A cross-platform, efficient and practical CSV/TSV toolkit in Golang
botond-sipos/biogo
biogo is a bioinformatics library for Go
botond-sipos/ensembl-compara
The Ensembl Compara Perl API and SQL schema
botond-sipos/hammerpede
A package for training strand-specific profile HMMs for primer sets from real Nanopore data
botond-sipos/isONclust2
A tool for de novo clustering of long transcriptomic reads
botond-sipos/manuscript-pat
PAT-seq manuscript
botond-sipos/paper-ng-sam
Pipeline for simulating NG-SAM experiments
botond-sipos/phylosim
An R package for the Monte Carlo simulation of sequence evolution
botond-sipos/rlsim
A package for simulating RNA-seq library preparation with parameter estimation
botond-sipos/simcopy
An R package simulating the evolution of copy number profiles along a tree
botond-sipos/spliced_bam2gff
botond-sipos/thist
A go package for generating online histograms and plotting them in the terminal and PDFs
botond-sipos/paper-pat-seq
botond-sipos/paper-rlsim
Analysis pipeline for assesing biasing factors in Illumina RNA-seq protocols through realistic simulations
botond-sipos/pcrcoal
pcrcoal is an R package implementing the coalescent approach to PCR simulation developed by Weiss and von Haeseler (NAR, 1997)
botond-sipos/pinfish
Tools to annotate genomes using long read transcriptomics data
botond-sipos/pipeline-nanopore-denovo-isoforms
Pipeline for de novo clustering of long transcriptomic reads
botond-sipos/pipeline-nanopore-ref-isoforms
Pipeline for annotating genomes using long read transcriptomics data with stringtie and other tools
botond-sipos/pipeline-polya-diff
Pipeline for testing shifts in poly(A) tail lengths estimated by nanopolish
botond-sipos/pipeline-polya-ng
Pipeline for calling poly(A) tail lengths from nanopore direct RNA data using nanopolish
botond-sipos/pipeline-transcriptome-de
Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
botond-sipos/pychopper
A tool to identify, orient, trim and rescue full length cDNA reads
botond-sipos/seqkit
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
botond-sipos/wub
Tools and software library developed by the ONT Applications group