iRegulon and i-cisTarget: Reconstructing Regulatory Networks Using Motif and Track Enrichment [0.03%]
基于基序和轨道富集的调控网络重构:iRegulon 和 i-cisTarget 系统
Annelien Verfaillie,Hana Imrichova,Rekins Janky et al.
Annelien Verfaillie et al.
Gene expression profiling is often used to identify genes that are co-expressed in a biological process or disease. Downstream analyses of co-expressed gene sets using bioinformatics methods can reveal candidate transcription factors (TF) t...
Andy Menzies,Jon W Teague,Adam P Butler et al.
Andy Menzies et al.
VAGrENT is a tool that provides biological context and effect prediction for genomic sequence variants. It annotates single base substitutions and small insertions and deletions by comparing them to reference information within or close to ...
cgpPindel: Identifying Somatically Acquired Insertion and Deletion Events from Paired End Sequencing [0.03%]
CGP-PINDEL：从配对末端测序中识别体细胞获得的插入和缺失事件
Keiran M Raine,Jonathan Hinton,Adam P Butler et al.
Keiran M Raine et al.
cgpPindel is a modified version of Pindel that is optimized for detecting somatic insertions and deletions (indels) in cancer genomes and other samples compared to a reference control. Post-hoc filters remove false positive calls, resulting...
Unix Survival Guide [0.03%]
UNIX实用技术指南
Lincoln D Stein
Lincoln D Stein
Most bioinformatics software has been designed to run on Linux and other Unix-like systems. Unix is different from most desktop operating systems because it makes extensive use of a text-only command-line interface. It can be a challenge to...
Alexandros Stamatakis
Alexandros Stamatakis
Inference of phylogenetic trees under the maximum likelihood (ML) criterion represents a routine task in biological data analysis. In this unit we describe how to plan analyses and use Randomized Accelerated Maximum Likelihood (RAxML) for p...
William R Pearson
William R Pearson
The characterization of new genomes based on their protein sets has been revolutionized by new sequencing technologies, but biologists seeking to exploit new sequence information are often frustrated by the challenges associated with accura...
Gary D Stormo
Gary D Stormo
Transcription factors (TFs) recognize and bind to specific DNA sequences. The specificity of a TF is usually represented as a position weight matrix (PWM). Several databases of DNA motifs exist and are used in biological research to address...
Using PepExplorer to Filter and Organize De Novo Peptide Sequencing Results [0.03%]
利用PepExplorer过滤和组织从头 peptide测序结果
Felipe da Veiga Leprevost,Valmir C Barbosa,Paulo Costa Carvalho
Felipe da Veiga Leprevost
PepExplorer aids in the biological interpretation of de novo sequencing results; this is accomplished by assembling a list of homolog proteins obtained by aligning results from widely adopted de novo sequencing tools against a target-decoy ...
Alexander Dobin,Thomas R Gingeras
Alexander Dobin
Mapping of large sets of high-throughput sequencing reads to a reference genome is one of the foundational steps in RNA-seq data analysis. The STAR software package performs this task with high levels of accuracy and speed. In addition to d...
Common File Formats [0.03%]
常用文件格式
Lauren Mills
Lauren Mills
An overview of the many file formats commonly used in bioinformatics and genome sequence analysis is presented, including various data file formats, alignment file formats, and annotation file formats. Example workflows illustrate how some ...