Pinned Repositories
needle
Needle (full name: Needle in a haystack) combines alignment and assembly for comprehensive virome, mycobiome, and eukaryome profiling on the strain level.
TAIR
The Atlas of Immunoglobulin Repertoires (TheAIR)
good.software
This is the GitHub repository for our recent study "A comprehensive analysis of the usability and archival stability of omics computational tools and resources." Please follow to the repository's wiki for more information and details on how this repository is connected to the paper.
HapIso
HapIso reconstructs the haploid transcriptome of a diploid organism from long single molecule reads
MiCoP
MiCoP is a method for high-accuracy profiling of viral and fungal metagenomic communities.
online.bioinformatics
recycle.RNA.seq
This project contains the links to the datasets, software and code that was used for our study "ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues"
rop
The Read Origin Protocol (ROP) is a computational protocol that aims to discover the source of all reads, including those originating from repeat sequences, recombinant B and T cell receptors, and microbial communities.
UMI-Reducer
A computational tool for processing and differentiating PCR duplicates from biological duplicates
undergraduates-in-genomics
The catalogue was prepared for our study "Involving undergraduates in genomics research to narrow the education-research gap"
smangul1's Repositories
smangul1/HapIso
HapIso reconstructs the haploid transcriptome of a diploid organism from long single molecule reads
smangul1/imrep.GTEx
Scripts and commands we used in our study : Profiling immunoglobulin repertoires across multiple human tissues by RNA Sequencing
smangul1/recycle.RNA.seq
This project contains the links to the datasets, software and code that was used for our study "ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues"
smangul1/ec
This project includes simulated and 'golden standard' datasets, software and scripts that we used to benchmark error correction tools
smangul1/euvipath-scripts
Scripts and commands we used in our study : Rapid and accurate metagenomic profiling of eukaryotic and viral pathogens across various habitats and human tissues
smangul1/GTEx.metadata
prepared metadata for GTEx project
smangul1/undergraduates-in-genomics
The catalogue was prepared for our study "Involving undergraduates in genomics research to narrow the education-research gap"
smangul1/best-benchmarking
Best practices for conducting benchmarking in the most comprehensive and reproducible way
smangul1/cmd
Miscellaneous scripts for hoffman2
smangul1/command-line-teaching
online catalogue of resources and papers aimed to provide first-time learners with basic knowledge of command line
smangul1/DE
DE package
smangul1/ec2
new ec
smangul1/ggpubr
'ggplot2' Based Publication Ready Plots
smangul1/hla-polysolver
Fork of the Polysolver project
smangul1/imrep-10x
10x
smangul1/imrep-cloud
ImReP is a computational method for rapid and accurate profiling of the adaptive immune repertoire from regular RNA-Seq data.
smangul1/Metagenomics-review
review to explain metagenomics
smangul1/MetaSUB-Inter-City-Challenge
The MetaSUB Inter-City Challenge presents the urban microbiomes of three cities. Compare organism fingerprints from public places across cities. Investigate organism sequences and biodiversity vs location.
smangul1/Microbe-scope.project
smangul1/mosdepth
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
smangul1/oda.cluster
scripts for oda cluster
smangul1/rarev
rarev
smangul1/raritet
smangul1/rop-fork1
smangul1/rough
Create graphics with a hand-drawn, sketchy, appearance
smangul1/submit.jobs
how to submit jobs on various clusters
smangul1/teach-cpp-autograding
smangul1/trinityrnaseq
Trinity RNA-Seq de novo transcriptome assembly
smangul1/UMI-Reducer-new
smangul1/UMI.project
scripts and data accompanying the paper