Smediterranea's repositories
Cho_Xi_Seqscope
Seqscope codes
DoubletFinder
R package for detecting doublets in single-cell RNA sequencing data
Filtlong
quality filtering tool for long reads
fineRADstructure
A package for population structure inference from RAD-seq data
getting-started-with-genomics-tools-and-resources
Unix, R and python tools for genomics and data science
GRAAL
(check out instaGRAAL for a faster, updated program!) This program is from Marie-Nelly et al., Nature Communications, 2014 (High-quality genome assembly using chromosomal contact data), also Marie-Nelly et al., 2013, PhD thesis (https://www.theses.fr/2013PA066714)
HapCUT2-1
software tools for haplotype assembly from sequence data
hic_qc
A (very) simple script to QC Hi-C data.
hicstuff
Simple library/pipeline to generate and handle Hi-C data.
HiFiAdapterFilt
Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz).
instaGRAAL
Large genome reassembly based on Hi-C data, continuation of GRAAL
juicebox_scripts
A collection of scripts for working with Hi-C data, Juicebox, and other genomic file formats
MetBrewer
Color palette package in R inspired by works at the Metropolitan Museum of Art in New York
nPhase
Ploidy agnostic phasing pipeline and algorithm
pb-assembly
PacBio Assembly Tool Suite: Reads in ⇨ Assembly out
pbbioconda
PacBio Secondary Analysis Tools on Bioconda
pbipa
Improved Phased Assembler
PseudotimeDE
A robust DE test method that accounts for the uncertainty in pseudotime inference
RISC
A R package for integrated scRNA-seq data analysis using the RPCI algorithm
SequelTools
new repo
training-collection
Collection of bioinformatics training materials
wtdbg2
Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly