scRNA-tools
Welcome to scRNA-tools! The scRNA-tools database is a catalogue of tools for analysing single-cell RNA sequencing data. View Tools The scRNA-tools database records details of software tools designed for analysing scRNA-seq data. Each tool is categorised according to the analysis tasks it can be used for.
CORA
CORA Massachusetts Institute of Technology (mit) Computer Science and Artificial Intelligence Laboratory (csail) Theory of Computation Group (toc) Berger Lab for Computation and Biology (compbio) Corresponding author for study: bab@mit.edu Queries regarding usage of CORA software: denizy@mit.edu A new implementation of CORA's homology table construction in the Seq programming language can be found
REST URLs for data retrieval < Search and browse < European Nucleotide Archive < EMBL-EBI
ENA Data Submission General Guide On ENA Data Submission How to Register a Study How to Register Samples Preparing Files for Submission How to Submit Raw Reads How to Submit Assemblies How to Submit Targeted Sequences How to Submit Other Analyses ENA Data Discovery & Retrieval General Guide on ENA Data Retrieval Viewing and Exploring ENA Records Search and Retrieval Programmatic Access How to Acce
PRINSEQ @ SourceForge.net
PRINSEQ. PReprocessing and INformation of SEQuence data. Easy and rapid quality control and data preprocessing. PRINSEQ can be used to filter, reformat, or trim your genomic and metagenomic sequence data. It generates summary statistics of your sequences in graphical and tabular format. It is easily configurable and provides a user-friendly interface. Input and output formats You can use data in F
tabix(1) manual page
NAME tabix – Generic indexer for TAB-delimited genome position files SYNOPSIS tabix [-0lf] [-p gff|bed|sam|vcf] [-s seqCol] [-b begCol] [-e endCol] [-S lineSkip] [-c metaChar] in.tab.bgz [region1 [region2 [...]]] DESCRIPTION Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file (in.tab.bgz.tbi or in.tab.bgz.csi) when region is absent from the command-line. The inp
Peak detectionソフトウェア
ChIP-seq解析におけるピークを検出するソフトウェアについての簡単なリスト。上位の方のリストは、ランダムに選択してきた２１報のChIP-seqに関する論文に載っていたものから、比較的引用数の多いものを取り上げた。選択した論文の内容について統計をとった最近のChIP-seqの解析手法のまとめについての記事を参照してほしい。被引用数は、手法について述べた論文の2010年度までの被引用数の合計。星の数は、単なる自分の好み。 Useq (http://useq.sourceforge.net/) [24 citation] +と-の間のピークのシフト距離を推定し、その半分の距離をそれぞれ3'方向に移動。windowサイズをシフトした距離＋標準偏差として、そのwindowでslidingさせた次の２つのスコアを計算する。(1) 単にwindow内のreadsの数。(2) ２項分布をもとにしたP
Moleculo technology: synthetic long reads for genome phasing, de novo sequencing
Moleculo, acquired by Illumina in late 2012, has developed an innovative technology for generating long reads that combines a new sample prep method and genome analysis tools. The technology breaks DNA into large fragments that are sequenced on standard Illumina sequencing systems for subsequent assembly into synthetic long reads using proprietary informatics. The Moleculo sample prep is a full en
RECOT: Read Coordinate Transformer
RECOT transforms coordinate of next-generation sequencer reads from your genome/gene to other species genome. RECOT is useful to compare RNA-seq, ChIP-seq and CLIP-seq sequences between closely-related species. Requirements (Data) Reads of your original species (1) Two different genomes (Your originally experimented species and target species) (2,4) Gene regions of your original genome in GFF form
RNA-eXpress
WELCOME Welcome to the RNA-eXpress home page. RNA-eXpress was designed as a user friendly solution to extract and annotate biologically important transcripts from next generation RNA sequencing data. This approach complements existing gene annotation databases by ensuring all transcripts present in the sample are considered for further analysis. The current stable release is available from the dow
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GitHub - lonsbio/fastqe: Redirection to the new FASTQE repo.
GitHub - macarthur-lab/igv_utils: utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.
GitHub - adaptivegenome/clusterseq: Measuring population dynamics in barcoded cell populations using high-throughput sequencing
GitHub - soh-i/cligb: cligb: Command line based genome browser for small RNA-seq data
Google Code Archive - Long-term storage for Google Code Project Hosting.
Justus-Liebig-Universität Gießen
GitHub - BenLangmead/comp-genomics-class: Code and examples for JHU Computational Genomics class
HTS format specifications
Google Code Archive - Long-term storage for Google Code Project Hosting.
Google Code Archive - Long-term storage for Google Code Project Hosting.
Google Code Archive - Long-term storage for Google Code Project Hosting.