nalomran

Nawaf A. Alomran's starred repositories

pandas

Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more

Language:PythonBSD-3-Clause43380 1110 26847

gatk

Official code repository for GATK versions 4 and up

Language:JavaNOASSERTION1682 155 4547

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

Language:CNOASSERTION1609 100 1263

picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

Language:JavaMIT971 159 806

bedtools2

bedtools - the swiss army knife for genome arithmetic

Language:CMIT928 58 831

ChIP-seq-analysis

ChIP-seq analysis notes from Ming Tang

Language:PythonMIT737 65 12

mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Language:NimMIT689 22 210

deepTools

Tools to process and analyze deep sequencing data.

Language:PythonNOASSERTION674 36 935

bowtie2

A fast and sensitive gapped read aligner

Language:C++GPL-3.0662 31 431

vcflib

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

Language:C++MIT616 39 271

vcftools

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

Language:C++LGPL-3.0498 32 191

SURVIVOR

Toolset for SV simulation, comparison and filtering

Language:C++MIT353 12 209

pybedtools

Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")

Language:PythonNOASSERTION301 16 293

bedops

:microscope: BEDOPS: high-performance genomic feature operations

Language:CNOASSERTION296 16 273

chip-seq-pipeline2

ENCODE ChIP-seq pipeline

Language:PythonMIT241 26 175

pysamstats

A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.

Language:Python190 12 100

Genrich

Detecting sites of genomic enrichment

Language:CMIT185 10 111

lollipops

Lollipop-style mutation diagrams for annotating genetic variations.

Language:GoGPL-3.0180 18 73

pyliftover

Pure-python implementation of UCSC liftOver genome coordinate conversion

Language:PythonMIT88 6 17

ATACseq

Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)

Language:ShellBSD-3-Clause74 7 6

biotoolsRegistry

biotoolsregistry : discovery portal for bioinformatics

Language:HTMLGPL-3.070 25 548

svtools

Tools for processing and analyzing structural variants.

Language:Python32 40

ENCODE_downloader

Downloader for ENCODE

Language:PythonBSD-3-Clause31 7 12

lollipops

This is the development fork - Stable code has been moved to ==>

Language:GoGPL-3.023 10

gtex

GTEx analysis scripts

Language:Python20 5 1

DANPOS3

Updated DANPOS2 to work with python3

Language:Python20 2 8

ENCODE-cCREs

Pipelines to create and analyze ENCODE candidate cis-Regulatory Elements

Language:Shell19 6 9

FunSeq2_DC

a modified version of FunSeq2 using new data context

Language:Perl13 20

mnaseseq

MNase-seq analysis pipeline using BWA and DANPOS2.

Language:NextflowMIT10 135 4

encode-data-usage-examples

Language:Jupyter NotebookMIT900