Results for "R"
Bio-Scripts
...t Cloning into 'nextsv'... remote: Counting objects: 369, done. remote: Total 369 (delta 0), re...1.2.7/CMakeFiles/zlibstatic.dir/gzclose.o [ 6%] Building C...^ /home/urbe/Tools/nextsv/aligners_and_c...s_and_callers/Sniffles-1.0.5/src/realign/SWCPU.cpp:30:71: war...2107 days ago
Install Python locally on shared Linux server !
#Install python to local directory #Firstly, I create a folder in my home directory, downloa...gz find ~/python -type d | xargs chmod 0755 cd Python-2.7.1...to specify where to put the #related output of make command,...by running the command: source ~/.bashrc_profile #You m...2106 days ago
Perl script to extract sequence by Ids from multifasta file !
#!/usr/bin/perl -w use strict; my $idsfile = "$ARGV[0]"; my $seqfile = "$ARGV[1]"; my %ids...= 1; } close FILE; local $/ = "\n>"; # read by FASTA record open FA...$_; my ($id) = $seq =~ /^>*(\S+)/; # parse ID as first word in FASTA h...2104 days ago
Installing Busco version 4.0.6
(base) jit@jit-HP-Pro-3335-MT: conda install -c bioconda -c conda-forge busco=4.0.6 Collecting package metadata (repodata.json): done Solving e...153 KB conda-forge r-pkgconfig-2.0.3 |...s-check bioconda/linux-64::perl-params-check-0.38-pl526_1...1461 days ago
- jitendra@jitendra-UNLOCK-INSTALL[SNP] wget https://github.com/broadinstitute/gatk/releases/dow...IlluminaBasecallsToSam (Picard) Transforms raw...ile. CollectIndependentReplicateMetrics (Picard) (BET...nce file. ReplaceSamHeader (Picard) R...
2084 days ago
- ➜ upgrade_oh_my_zsh Updating Oh My Zsh remote: Counting objects: 484, done. remote: Compressing objects: 100% (243/243), done. remote: Total 484 (delta 290),...s/per-directory-history/per-directory-history.zsh | 2 +-..._/ Hooray! Oh My Zsh has been updated...
2083 days ago
Perl script to extract a sequence from multifasta with range !
# filterfastarange.pl #!/usr/bin/perl use strict; use warnings; #perl filterfastarange.pl 301 600...s-gt300-lte600.fasta my $minlen = shift or die "Error: `minlen` paramete...my @chunk = split /\n/; my $header = shift @chunk; my $...2074 days ago
Perl script to break the contigs by 'N'
#!/usr/bin/perl -w use Bio::SeqIO; use strict; my $fasta = Bio::SeqIO->new( -file => "$ARGV[0].parts.fasta",-format=>'f...eq = uc $seq; #now all bases are in uppercase #Searches f...1; if ($#regions>=0) { for (my $i=0;$itrunc($cini,$cend)...2071 days ago
- library(vcfR) # Input the files. vcf
2069 days ago
#Install older version of R Packages !
#Install older version of R Packages ! require(devtools) install_version("IdeoViz", version = "0.9.1", repos = "http://cran.us.r-project.org")2068 days ago
