Smith Lab (@smithlabcode)
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smithlabcode

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  • Stars
    star
    396
  • Global Org. Rank 27,514 (Top 9 %)
  • Registered over 10 years ago
  • Most used languages
    C++
         68.2 %
    Python
         9.1 %
    R
         9.1 %
    Jupyter Notebook
         4.5 %
    C
         4.5 %
    HTML
         4.5 %
  • Location 🇺🇸 United States
  • Country Total Rank 19,227
  • Country Ranking
    C++
         1,354
    R
         1,544
    HTML
         1,808

Top repositories

1

falco

A C++ drop-in replacement of FastQC to assess the quality of sequence read data
HTML
98
star
2

preseq

Software for predicting library complexity and genome coverage in high-throughput sequencing.
C++
77
star
3

methpipe

A pipeline for analyzing DNA methylation data from bisulfite sequencing.
C++
66
star
4

ribotricer

A tool for accurately detecting actively translating ORFs from Ribo-seq data
Python
31
star
5

dnmtools

Tools for analyzing DNA methylation data
C++
27
star
6

piranha

Piranha is a peak-caller for CLIP- and RIP-seq data
C++
17
star
7

walt

WALT is a read mapping program for bisulfite sequencing DNA methylation studies.
C++
17
star
8

preseqR

An R package for estimating library complexity
R
12
star
9

abismal

Abismal is a mapper of FASTQ bisulfite-converted short reads (between 50 and 1000 bases) to a FASTA reference genome.
C++
12
star
10

riborex

Riborex: Fast and flexible identification of differential translation from Ribo-seq data
R
9
star
11

ribotricer-results

Results and scripts for benchmarking ribotricer for translating ORF detection from Ribo-seq data
Jupyter Notebook
8
star
12

rmap

Short reads mapper for next-generation sequencing data (DNA-seq, BS-seq, etc)
C++
5
star
13

rseg

A software tool to identify dispersed epigenetic regions from ChIP-seq data
C
5
star
14

smithlab_cpp

C++ code library that includes functions used in many of the Smith lab projects
C++
4
star
15

smurfseq_scripts

Scripts and some documentation for how we did CNV analysis using SMURF-seq reads and how we generated simulated data to evaluate mapping performance.
Python
4
star
16

amordad

Amordad is a database engine for high dimensional data
C++
3
star
17

radmeth

C++
3
star
18

Epiphyte

A package for estimating phylogenetic tree for epigenomes (DNA methylation primarily) from multiple species.
C++
3
star
19

zagros

Zagros is an algorithm for motif discovery in CLIP-seq data
C++
2
star
20

mlml

Simultaneously estimate hydroxymethylation (5hmC) and methylation (5mC) levels
C++
2
star
21

epievo

Programs for simulating and inferring epigenome evolution.
C++
1
star
22

utils

A collection of utility programs that might be useful to someone.
C++
1
star