smediterranea Goto Github PK

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

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

Performs haplotype assembly from genomic DNA sequence reads for a single individual using a maximum-likelihood based approach. Performs well on diverse NGS technologies, including long read data and Hi-C.

hapcut2-1

software tools for haplotype assembly from sequence data

hapi

Chromosome-length haplotype inference using genotype data of single gamete cells

hic-box

GUI-based pipeline for Hi-C data processing and visualization

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

lja

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

qtlmapping

repeatscout

The RepeatScout 1.0.5, written by Pevzner et al., source code for browsing. The official release and more information are available at http://bix.ucsd.edu/repeatscout/

risc

A R package for integrated scRNA-seq data analysis using the RPCI algorithm