Pinned Repositories
Arena_R_Code
Cho_Xi_Seqscope
Seqscope codes
COPILOT
Single cell RNA-seq preprocessing tool for gene-by-cell matrices of UMI counts. It is recommended to use the raw spliced and unpliced counts matrices produced by scKB pipeline as the input of copilot.
DipAsm
doubletD
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
finishingTool
finshingTool
Smediterranea's Repositories
Smediterranea/COPILOT
Single cell RNA-seq preprocessing tool for gene-by-cell matrices of UMI counts. It is recommended to use the raw spliced and unpliced counts matrices produced by scKB pipeline as the input of copilot.
Smediterranea/Arena_R_Code
Smediterranea/Cho_Xi_Seqscope
Seqscope codes
Smediterranea/DipAsm
Smediterranea/doubletD
Smediterranea/DoubletFinder
R package for detecting doublets in single-cell RNA sequencing data
Smediterranea/Filtlong
quality filtering tool for long reads
Smediterranea/fineRADstructure
A package for population structure inference from RAD-seq data
Smediterranea/getting-started-with-genomics-tools-and-resources
Unix, R and python tools for genomics and data science
Smediterranea/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)
Smediterranea/HapCUT2-1
software tools for haplotype assembly from sequence data
Smediterranea/hic_qc
A (very) simple script to QC Hi-C data.
Smediterranea/hicstuff
Simple library/pipeline to generate and handle Hi-C data.
Smediterranea/HiFiAdapterFilt
Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz).
Smediterranea/instaGRAAL
Large genome reassembly based on Hi-C data, continuation of GRAAL
Smediterranea/juicebox_scripts
A collection of scripts for working with Hi-C data, Juicebox, and other genomic file formats
Smediterranea/LJA
Smediterranea/MetBrewer
Color palette package in R inspired by works at the Metropolitan Museum of Art in New York
Smediterranea/nPhase
Ploidy agnostic phasing pipeline and algorithm
Smediterranea/pb-assembly
PacBio Assembly Tool Suite: Reads in ⇨ Assembly out
Smediterranea/pbbioconda
PacBio Secondary Analysis Tools on Bioconda
Smediterranea/pbipa
Improved Phased Assembler
Smediterranea/PseudotimeDE
A robust DE test method that accounts for the uncertainty in pseudotime inference
Smediterranea/QTLmapping
Smediterranea/RISC
A R package for integrated scRNA-seq data analysis using the RPCI algorithm
Smediterranea/SequelTools
new repo
Smediterranea/STtools
Smediterranea/training-collection
Collection of bioinformatics training materials
Smediterranea/tricycle
Smediterranea/wtdbg2
Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly