nalomran
Bioinformatician & Programmer. I utilize programming in Python and/or R to tackle problems related to Genomics & RNA-Seq. I also like to do Data Science.
nalomran's Stars
broadinstitute/gatk
Official code repository for GATK versions 4 and up
khuranalab/FunSeq2_DC
a modified version of FunSeq2 using new data context
joiningdata/lollipops
Lollipop-style mutation diagrams for annotating genetic variations.
pbnjay/lollipops
This is the development fork - Stable code has been moved to ==>
ENCODE-DCC/chip-seq-pipeline2
ENCODE ChIP-seq pipeline
arq5x/bedtools2
bedtools - the swiss army knife for genome arithmetic
deeptools/deepTools
Tools to process and analyze deep sequencing data.
brentp/mosdepth
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
alimanfoo/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.
tobiasrausch/ATACseq
Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
nf-core/mnaseseq
MNase-seq analysis pipeline using BWA and DANPOS2.
BenLangmead/bowtie2
A fast and sensitive gapped read aligner
sklasfeld/DANPOS3
Updated DANPOS2 to work with python3
jsh58/Genrich
Detecting sites of genomic enrichment
crazyhottommy/ChIP-seq-analysis
ChIP-seq analysis notes from Ming Tang
kundajelab/ENCODE_downloader
Downloader for ENCODE
daler/pybedtools
Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
weng-lab/ENCODE-cCREs
Pipelines to create and analyze ENCODE candidate cis-Regulatory Elements
ENCODE-DCC/encode-data-usage-examples
hall-lab/gtex
GTEx analysis scripts
pandas-dev/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
bio-tools/biotoolsRegistry
biotoolsregistry : discovery portal for bioinformatics
broadinstitute/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.
konstantint/pyliftover
Pure-python implementation of UCSC liftOver genome coordinate conversion
samtools/samtools
Tools (written in C using htslib) for manipulating next-generation sequencing data
vcftools/vcftools
A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.
fritzsedlazeck/SURVIVOR
Toolset for SV simulation, comparison and filtering
ctsa/svtools
Tools for processing and analyzing structural variants.
vcflib/vcflib
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
bedops/bedops
:microscope: BEDOPS: high-performance genomic feature operations