yimsea Goto Github PK

annotation-and-image-markup

Annotation and Image Markup (AIM) is the first project to propose and create a standard means of adding information and knowledge to an image in a clinical environment, so that image content can be easily and automatically searched.

ballgown

Bioconductor package "ballgown", devel version. Isoform-level differential expression analysis in R.

bedtools2

A powerful toolset for genome arithmetic.

blasr

BLASR: The PacBio® long read aligner

breakmer

A method to identify structural variation from sequencing data in target regions

cdna_primer

Scripts for processing PacBio transcriptome (Iso-Seq) data

centrifuge

Classifier for metagenomic sequences

chimpipe

ChimPipe: Accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data

clamms

CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data.

cohort_qc

Quality control of fastq and bam files at cohort level

common-workflow-language

Repository for CWL Specifications. Use https://www.biostars.org/t/cwl/ for support.

coseq

Co-Expression Analysis of Sequencing Data

d3

A JavaScript visualization library for HTML and SVG.

dada2

Accurate sample inference from amplicon data with single nucleotide resolution

devnet

The DevNet project on github stores the PacBio DevNet website.

emsar

EMSAR quantifies transcripts from RNA-seq data (Citation : Lee et al., BMC Bioinformatics 2015, 16:278, http://www.biomedcentral.com/1471-2105/16/278)

fastquick

Ultra Fast NGS Data QC Tool

freebayes

Bayesian haplotype-based polymorphism discovery and genotyping.

g3plot-1

g3plot release 1 from intel

genomicconsensus

PacBio® variant and consensus caller (Quiver algorithm)

ghost-tree

gscholar

Query Google Scholar with Python

hbar-dtk

Hierarchical based assembler development toolkit

igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

ipanda

insilico Pathway Activation Network Decomposition Analysis (iPANDA) package. Owned by Insilico Medicine Inc. iPANDA is a pathway analysis method that aids interpretation of large-scale gene expression data. The method introduced here includes coexpression analysis and gene importance estimation to robustly identify relevant pathways and biomarkers for patient stratification.

jaffa

JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions

koeken

A Linear Discriminant Analysis Effect Size (LEfSe) wrapper.

koreader

An ebook reader application supporting PDF, DjVu, EPUB, FB2 and many more formats, running on Cervantes, Kindle, Kobo, PocketBook and Android devices

kpal

Analysis toolkit and programming library for k-mer profiles

learn-python3

Learn Python 3 Sample Code