Merge branch 'main' of https://github.com/HYsxe/PRINT into main

[tutorial]:https://github.com/HYsxe/PRINT/blob/main/analyses/BMMCTutorial/BMMCVignette.pdf

Before running the tutorial, please download the pre-computed bias files from https://zenodo.org/record/7121027#.ZCbw4uzMI8N and put it in the data/shared/precomputedTn5Bias folder.

### 4. References

Hu et al., Multi-scale chromatin footprinting reveals wide-spread encoding of CRE substructures

If you have any questions, please feel free to open an issue. You are also welcome to email me at yanhu@g.harvard.edu. We appreciate everyone's contribution!

### 7. Comming soon:

Currently the tool is implemented in R, which doesn't handle certein computation in the most efficient way. We are working on a ultra-fast python package which will be released soon. Stay tuned!

Softwares:

samtools==1.10

bedtools==2.26.0

macs2==2.1.1.20160309

TOBIAS==0.13.2

Bowtie2==2.3.4.1

HINT==0.13.2

R==4.1.0

Python==3.8.16

Python packages:

tensorflow==2.6.2

Bio==1.5.5

h5py==2.10.0

keras==2.11.0

keras_nightly==2.5.0.dev2021032900

matplotlib==3.5.1

numpy==1.19.5

palantir==1.0.0

pandas==1.5.3

pybedtools==0.8.1

pyranges==0.0.120

pysam==0.18.0

scikit_learn==1.2.1

scipy==1.7.3

seaborn==0.11.2

torch==1.13.1

tqdm==4.62.3

R packages:

assertthat==0.2.1

base64enc==0.1-3

Biobase==2.52.0

BiocGenerics==0.38.0

BiocIO==1.2.0

BiocParallel==1.26.2

Biostrings==2.60.2

bit==4.0.4

bit64==4.0.5

bitops==1.0-7

BuenColors==0.5.6

Cairo==1.5-12.2

caTools==1.18.2

circlize==0.4.13

cladoRcpp==0.15.1

cli==3.2.0

clue==0.3-59

cluster==2.1.2

codetools==0.2-18

collapse==1.5.3

colorspace==2.0-3

compiler==4.1.3

ComplexHeatmap==2.8.0

crayon==1.5.0

data.table==1.14.2

DBI==1.1.2

DelayedArray==0.18.0

digest==0.6.29

doParallel==1.0.16

doSNOW==1.0.19

dplyr==1.0.8

ellipsis==0.3.2

evaluate==0.15

fansi==1.0.2

farver==2.1.0

fastmap==1.1.0

foreach==1.5.1

generics==0.1.2

GenomeInfoDb==1.28.4

GenomeInfoDbData==1.2.6

GenomicAlignments==1.28.0

GenomicRanges==1.44.0

GetoptLong==1.0.5

ggplot2==3.3.3

GlobalOptions==0.1.2

glue==1.6.2

gtable==0.3.0

gtools==3.9.2

hdf5r==1.3.3

htmltools==0.5.2

IRanges==2.26.0

iterators==1.0.13

jsonlite==1.8.0

keras==2.4.0

knitr==1.37

labeling==0.4.2

lattice==0.20-45

lifecycle==1.0.1

magick==2.7.2

magrittr==2.0.2

MASS==7.3-55

Matrix==1.4-0

MatrixGenerics==1.4.3

matrixStats==0.61.0

munsell==0.5.0

patchwork==1.1.1

pbapply==1.4-3

pbmcapply==1.5.0

pillar==1.7.0

pkgconfig==2.0.3

png==0.1-7

purrr==0.3.4

R6==2.5.1

RColorBrewer==1.1-3

Rcpp==1.0.7

RcppArmadillo==0.11.0.0.0

RcppEigen==0.3.3.9.1

RCurl==1.98-1.3

restfulr==0.0.13

reticulate==1.20

rjson==0.2.21

rlang==1.0.2

rmarkdown==2.13

Rsamtools==2.8.0

rstudioapi==0.13

rtracklayer==1.52.1

S4Vectors==0.30.2

scales==1.2.0

shape==1.4.6

snow==0.4-3

stringi==1.7.6

stringr==1.4.0

SummarizedExperiment==1.22.0

tensorflow==2.5.0

tfruns==1.5.0

tibble==3.1.6

tidyselect==1.1.2

tools==4.1.3

utf8==1.2.2

vctrs==0.3.8

whisker==0.4

withr==2.5.0

xfun==0.30

XML==3.99-0.9

XVector==0.32.0

yaml==2.3.5

zeallot==0.1.0

zlibbioc==1.38.0