A collection of useful bioinformatics scripts. Contribute to lazappi/binf-scripts development by creating an account on GitHub.
Contribute to NCBI-Hackathons/Ultrafast_Mapping_CSHL development by creating an account on GitHub. SRA Tools. Contribute to ncbi/sra-tools development by creating an account on GitHub. An automated protocol to extract variation or expression from public NGS datasets - NCBI-Hackathons/deSRA Basic RNAseq pipeline, from downloading Fastq files to DEG and GO analysis. Coded in bash, Perl and R - alfonsosaera/RNAseq A Kotlin/Java library to submit Variant Call Format (VCF) and CRAM files to the European Nucleotide Archive (ENA) - rror/ena-submit It additionally contains pre-processed .bam and .bai files in case you would like to try only Rcount and to skip the download and alignment part of the tutorial (in this case go to section 2.4). Assay for Transposase Accessible Chromatin (ATAC-seq) is an open chromatin profiling assay that is adapted to interrogate chromatin accessibility from small cell numbers. ATAC-seq surmounted a major technical barrier and enabled epigenome…
Allele-specific Binding from Chip-seq. Contribute to mlupien/ABC development by creating an account on GitHub. Nextflow pipeline for ChIP-seq analysis. Contribute to Dowell-Lab/ChIP-Flow development by creating an account on GitHub. This repository contains our CellTag CloneHunter R package for clone-calling. - babiddy/CloneHunter SRA Tools. Contribute to ncbi/sra-tools development by creating an account on GitHub. NCBI claims to have fixed the issue but if users encounter errors, we strongly suggest that those working with the data download and realign the fastq files above rather than using the files deposited in the SRA.
Basic RNAseq pipeline, from downloading Fastq files to DEG and GO analysis. Coded in bash, Perl and R - alfonsosaera/RNAseq A Kotlin/Java library to submit Variant Call Format (VCF) and CRAM files to the European Nucleotide Archive (ENA) - rror/ena-submit It additionally contains pre-processed .bam and .bai files in case you would like to try only Rcount and to skip the download and alignment part of the tutorial (in this case go to section 2.4). Assay for Transposase Accessible Chromatin (ATAC-seq) is an open chromatin profiling assay that is adapted to interrogate chromatin accessibility from small cell numbers. ATAC-seq surmounted a major technical barrier and enabled epigenome… It is not recommended to select multiple files for simultaneous download from the Files page. Web Browsers have hardwired limitations on the number of simultaneous downloads that are allowed. RNA-seq Viewer Team at the NCBI-assisted Boston Genomics Hackathon - NCBI-Hackathons/rnaseqview BAM files undergo consensus construction through the workflow illustrated above. Output BAMs are grouped according to type of error suppression (SSCS vs DCS) and whether Singleton Correction (SC) was implemented.
Tools to search through the Sequence Read Archive using Xsede's Jetstream - linsalrob/SearchSRA
For example, you can find the SRA file SRR390728.sra in ~/ncbi/sra and the resource files in ~/ncbi/refseq. Then you can run other SRA tools, e.g. fastq-dump on computing nodes. Presented December 17, 2015. This video shows you how to display, search, and download individual and genotype level data through the 1000 Genomes Browser, aAncient RNA from Late Pleistocene permafrost and historical…https://journals.plos.org/plosbiology/articleAncient DNA is known to survive in cold environments for tens of millennia, but it is assumed that ancient RNA could not persist in such a way due to its relative instability. However, this study shows that under permafrost conditions… This repository contains the CellTag data analysis R package to support clone calling and lineage reconstruction. - morris-lab/CellTagR SRA Tools. Contribute to ncbi/sra-tools development by creating an account on GitHub. Tools for Rnaseq analysis take file from SRA file to Fastq, run QC, map to genome and find DE genes. - BradyLab/Rnaseq Allele-specific Binding from Chip-seq. Contribute to mlupien/ABC development by creating an account on GitHub. Nextflow pipeline for ChIP-seq analysis. Contribute to Dowell-Lab/ChIP-Flow development by creating an account on GitHub.