diff --git a/bin/hicpro2higlass.sh b/bin/hicpro2higlass.sh
new file mode 100755
index 0000000000000000000000000000000000000000..5cc09b773e9dc016fd0bf1d95a023e3b4bb29054
--- /dev/null
+++ b/bin/hicpro2higlass.sh
@@ -0,0 +1,264 @@
+#!/bin/bash
+
+## HiC-Pro
+## Copyleft 2017 Institut Curie
+## Author(s): Nicolas Servant
+## Contact: nicolas.servant@curie.fr
+## This software is distributed without any guarantee under the terms of the BSD licence
+
+##
+## First version of converter between HiCPro and higlass.
+## The cooler python package should be properly installed, as well as the higlass software
+##
+
+##
+## A few notes about higlass
+##
+## docker run will install the docker image and start it
+## sudo docker run --detach --publish 8888:80 --volume ~/hg-data:/data --volume ~/hg-tmp:/tmp --name higlass-container gehlenborglab/higlass
+## sudo docker start higlass-container
+## sudo docker ps -all
+##
+## Once higlass is installed, you can just run it using
+## sudo docker start higlass-container
+## higlass will then be available at http://localhost:8888
+##
+
+###########################
+## trap handler
+###########################
+function trap_error()
+{
+ echo "Error: $1 - line $2 - exit status of last command: $?. Exit" >&2
+ exit 1
+}
+
+function trap_exit()
+{
+ ##Since bash-4.0 $LINENO is reset to 1 when the trap is triggered
+ if [ "$?" != "0" ]; then
+ echo "Error: exit status detected. Exit." >&2
+ fi
+
+ if [[ ! -z ${tmp_dir} && -e ${tmp_dir} ]]; then
+ echo -e "Cleaning temporary folders ..." >&2
+ /bin/rm -rf ${tmp_dir}
+ fi
+}
+
+trap 'trap_error "$0" "$LINENO"' ERR
+trap 'trap_exit' 0 1 2 3
+
+set -E ## export trap to functions
+set -o pipefail ## trace ERR through pipes
+
+## 0 =
+## 1 >
+## 2 <
+vercomp () {
+ if [[ $1 == $2 ]]
+ then
+ return 0
+ fi
+ local IFS=.
+ local i ver1=($1) ver2=($2)
+ # fill empty fields in ver1 with zeros
+ for ((i=${#ver1[@]}; i<${#ver2[@]}; i++))
+ do
+ ver1[i]=0
+ done
+
+ for ((i=0; i<${#ver1[@]}; i++))
+ do
+ if [[ -z ${ver2[i]} ]]
+ then
+ # fill empty fields in ver2 with zeros
+ ver2[i]=0
+ fi
+ if ((10#${ver1[i]} > 10#${ver2[i]}))
+ then
+ echo 1
+ fi
+ if ((10#${ver1[i]} < 10#${ver2[i]}))
+ then
+ echo 2
+ fi
+ done
+ echo 0
+}
+
+function usage {
+ echo -e "usage : hicpro2higlass -i INPUT -r RESOLUTION -c CHROMSIZE [-n] [-o ODIR] [-t TEMP] [-h]"
+ echo -e "Use option -h|--help for more information"
+}
+
+function help {
+ usage;
+ echo
+ echo "Generate Higlass input file from HiC-Pro results"
+ echo "See https://github.com/hms-dbmi/higlass-website for details about Higlass"
+ echo "---------------"
+ echo "OPTIONS"
+ echo
+ echo " -i|--input INPUT : allValidPairs or matrix file generated by HiC-Pro"
+ echo " -r|--res RESOLUTION : .matrix file resolution or maximum resolution to reach from the .allValidPairs input file"
+ echo " -c|--chrom CHROMSIZE : chromosome size file"
+ echo " [-n|--norm] : run cooler matrix balancing algorithm"
+ echo " [-o|--out] : output path. Default is current path"
+ echo " [-t|--temp] TEMP : path to tmp folder. Default is current path"
+ echo " [-h|--help]: help"
+ exit;
+}
+
+
+if [ $# -lt 1 ]
+then
+ usage
+ exit
+fi
+
+# Transform long options to short ones
+for arg in "$@"; do
+ shift
+ case "$arg" in
+ "--input") set -- "$@" "-i" ;;
+ "--bed") set -- "$@" "-b" ;;
+ "--res") set -- "$@" "-r" ;;
+ "--chrom") set -- "$@" "-c" ;;
+ "--out") set -- "$@" "-o" ;;
+ "--temp") set -- "$@" "-t" ;;
+ "--norm") set -- "$@" "-n" ;;
+ "--help") set -- "$@" "-h" ;;
+ *) set -- "$@" "$arg"
+ esac
+done
+
+INPUT_HICPRO=""
+INPUT_BED=""
+NORMALIZE=0
+CHROMSIZES_FILE=""
+RES=10000
+OUT="./"
+TEMP="./"
+
+while getopts ":i:b:c:r:o:t:nh" OPT
+do
+ case $OPT in
+ i) INPUT_HICPRO=$OPTARG;;
+ b) INPUT_BED=$OPTARG;;
+ n) NORMALIZE=1;;
+ c) CHROMSIZES_FILE=$OPTARG;;
+ r) RES=$OPTARG;;
+ o) OUT=$OPTARG;;
+ t) TEMP=$OPTARG;;
+ h) help ;;
+ \?)
+ echo "Invalid option: -$OPTARG" >&2
+ usage
+ exit 1
+ ;;
+ :)
+ echo "Option -$OPTARG requires an argument." >&2
+ usage
+ exit 1
+ ;;
+ esac
+done
+
+if [[ -z $INPUT_HICPRO ]];
+then
+ usage
+ exit
+fi
+
+if [[ ! -e $CHROMSIZES_FILE ]]; then
+ echo -e "$CHROMSIZES_FILE file not found. Exit"
+ exit 1
+fi
+
+## Detect input data type
+DATATYPE=""
+if [[ $INPUT_HICPRO == *.mat* ]]; then
+ DATATYPE="MATRIX"
+elif [[ $INPUT_HICPRO == *allValidPairs* || $INPUT_HICPRO == *validPairs* ]]; then
+ DATATYPE="VALID"
+else
+ echo -e "Unknown input data type. Expect .matrix or _allValidPairs input files."
+ exit 1
+fi
+echo -e "$DATATYPE input file detected ..."
+
+## Check cooler version
+which cooler > /dev/null;
+if [ $? != "0" ]; then
+ echo -e "Cooler is not installed or is not in your $PATH. See https://github.com/mirnylab/cooler for details."
+ exit 1;
+fi
+
+COOLER_VERSION=$(cooler --version 2>&1 | awk '{print $NF}')
+echo "Cooler version $COOLER_VERSION detected ..."
+cres=$(vercomp ${COOLER_VERSION} "0.7.6")
+if [[ $cres == "2" ]]; then
+ echo "Cooler version must be >= 0.7.6 ! Stop."
+ exit 1
+fi
+
+if [[ $DATATYPE == "VALID" ]]; then
+ which pairix > /dev/null;
+ if [ $? != "0" ]; then
+ echo -e "Pairix is not installed or is not in your PATH. See https://github.com/4dn-dcic/pairix."
+ exit 1;
+ fi
+fi
+
+echo -e "\nGenerating .cool files ..."
+tmp_dir=${TEMP}/_tmp$$
+mkdir -p $tmp_dir
+
+if [[ $DATATYPE == "MATRIX" ]]; then
+ out=$(basename $INPUT_HICPRO | sed -e 's/.mat.*/.cool/')
+
+ cooler makebins $CHROMSIZES_FILE $RES > $tmp_dir/bins.bed
+ cooler load -f coo --one-based $tmp_dir/bins.bed $INPUT_HICPRO $tmp_dir/$out
+
+ echo -e "\nZoomify .cool file ..."
+ if [[ $NORMALIZE == 1 ]]; then
+ cooler zoomify --balance $tmp_dir/$out
+ else
+ cooler zoomify --no-balance $tmp_dir/$out
+ fi
+ out=$(basename $INPUT_HICPRO | sed -e 's/.mat.*/.mcool/')
+
+elif [[ $DATATYPE == "VALID" ]]; then
+ out=$(basename $INPUT_HICPRO | sed -e 's/.allValidPairs.*/.cool/')
+
+ awk '{OFS="\t";print $2,$3,$4,$5,$6,$7,1}' $INPUT_HICPRO | sed -e 's/+/1/g' -e 's/-/16/g' > $tmp_dir/contacts.txt
+ cooler csort --nproc 2 -c1 1 -p1 2 -s1 3 -c2 4 -p2 5 -s2 6 \
+ -o $tmp_dir/contacts.sorted.txt.gz \
+ $tmp_dir/contacts.txt \
+ $CHROMSIZES_FILE
+
+ cooler makebins $CHROMSIZES_FILE $RES > $tmp_dir/bins.bed
+ cooler cload pairix $tmp_dir/bins.bed $tmp_dir/contacts.sorted.txt.gz $tmp_dir/$out
+
+ echo -e "\nZoomify .cool file ..."
+ if [[ $NORMALIZE == 1 ]]; then
+ cooler zoomify --balance $tmp_dir/$out
+ else
+ cooler zoomify --no-balance $tmp_dir/$out
+ fi
+ out=$(basename $INPUT_HICPRO | sed -e 's/.allValidPairs.*/.mcool/')
+fi
+
+## mv to out
+mv $tmp_dir/*cool ${OUT}/
+
+## clean
+/bin/rm -rf $tmp_dir
+
+echo -e "\nCooler file generated with success ..."
+echo "Please copy the file $out in your Higlass input directory and run :"
+echo "sudo docker exec higlass-container python higlass-server/manage.py ingest_tileset --filename /tmp/$out --datatype matrix --filetype cooler"
+
+
+
diff --git a/bin/ice b/bin/ice
new file mode 100755
index 0000000000000000000000000000000000000000..10f5f224a6064961a04ac2c09bc5b29286bf5484
--- /dev/null
+++ b/bin/ice
@@ -0,0 +1,124 @@
+#! /usr/bin/env python
+
+import sys
+import argparse
+import numpy as np
+from scipy import sparse
+
+import iced
+from iced.io import loadtxt, savetxt
+
+
+parser = argparse.ArgumentParser("ICE normalization")
+parser.add_argument('filename',
+ metavar='File to load',
+ type=str,
+ help='Path to file of contact counts to load')
+parser.add_argument("--results_filename",
+ "-r",
+ type=str,
+ default=None,
+ help="results_filename")
+parser.add_argument("--filtering_perc", "-f",
+ type=float,
+ default=None,
+ help="Percentage of reads to filter out")
+parser.add_argument("--filter_low_counts_perc",
+ type=float,
+ default=0.02,
+ help="Percentage of reads to filter out")
+parser.add_argument("--filter_high_counts_perc",
+ type=float,
+ default=0,
+ help="Percentage of reads to filter out")
+parser.add_argument("--remove-all-zeros-loci", default=False,
+ action="store_true",
+ help="If provided, all non-interacting loci will be "
+ "removed prior to the filtering strategy chosen.")
+parser.add_argument("--max_iter", "-m", default=100, type=int,
+ help="Maximum number of iterations")
+parser.add_argument("--eps", "-e", default=0.1, type=float,
+ help="Precision")
+parser.add_argument("--dense", "-d", default=False, action="store_true")
+parser.add_argument("--output-bias", "-b", default=False, help="Output the bias vector")
+parser.add_argument("--verbose", "-v", default=False)
+
+
+args = parser.parse_args()
+filename = args.filename
+
+# Deprecating filtering_perc option
+filter_low_counts = None
+if "--filtering_perc" in sys.argv:
+ DeprecationWarning(
+ "Option '--filtering_perc' is deprecated. Please use "
+ "'--filter_low_counts_perc' instead.'")
+ # And print it again because deprecation warnings are not displayed for
+ # recent versions of python
+ print "--filtering_perc is deprecated. Please use filter_low_counts_perc"
+ print "instead. This option will be removed in ice 0.3"
+ filter_low_counts = args.filtering_perc
+if "--filter_low_counts_perc" in sys.argv and "--filtering_perc" in sys.argv:
+ raise Warning("This two options are incompatible")
+if "--filtering_perc" is None and "--filter_low_counts_perc" not in sys.argv:
+ filter_low_counts_perc = 0.02
+elif args.filter_low_counts_perc is not None:
+ filter_low_counts_perc = args.filter_low_counts_perc
+
+if args.verbose:
+ print("Using iced version %s" % iced.__version__)
+ print "Loading files..."
+
+# Loads file as i, j, counts
+i, j, data = loadtxt(filename).T
+
+# Detecting whether the file is 0 or 1 based.
+if min(i.min(), j.min()) == 0:
+ index_base = 0
+ N = max(i.max(), j.max()) + 1
+ counts = sparse.coo_matrix((data, (i, j)), shape=(N, N), dtype=float)
+else:
+ index_base = 1
+ N = max(i.max(), j.max())
+ counts = sparse.coo_matrix((data, (i - 1, j - 1)), shape=(N, N), dtype=float)
+
+if args.dense:
+ counts = np.array(counts.todense())
+else:
+ counts = sparse.csr_matrix(counts)
+
+if args.verbose:
+ print "Normalizing..."
+
+if filter_low_counts_perc != 0:
+ counts = iced.filter.filter_low_counts(counts,
+ percentage=filter_low_counts_perc,
+ remove_all_zeros_loci=args.remove_all_zeros_loci,
+ copy=False, sparsity=False, verbose=args.verbose)
+if args.filter_high_counts_perc != 0:
+ counts = iced.filter.filter_high_counts(
+ counts,
+ percentage=args.filter_high_counts_perc,
+ copy=False)
+
+counts, bias = iced.normalization.ICE_normalization(
+ counts, max_iter=args.max_iter, copy=False,
+ verbose=args.verbose, eps=args.eps, output_bias=True)
+
+if args.results_filename is None:
+ results_filename = ".".join(
+ filename.split(".")[:-1]) + "_normalized." + filename.split(".")[-1]
+else:
+ results_filename = args.results_filename
+
+counts = sparse.coo_matrix(counts)
+
+if args.verbose:
+ print "Writing results..."
+
+savetxt(
+ results_filename, counts.col + index_base, counts.row + index_base, counts.data)
+
+
+if args.output_bias:
+ np.savetxt(results_filename + ".biases", bias)