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Shruti Paniwala
@shruti
Shruti Paniwala
A Bioinformatician
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The Wire
Shruti Paniwala
Shruti Paniwala's wire posts
Shruti Paniwala
@shruti
Thread
By
Shruti Paniwala
2566 days ago
Chi squared test
https:/
/
edwards.sdsu.edu/
research/
calculating-chi-squared-wiht-perl/
#Perl
#Chi
#Probability
Shruti Paniwala
@shruti
Thread
By
Shruti Paniwala
2587 days ago
Data structure with R
http:/
/
staff.washington.edu/
jon/
dsa-perl/
dsa-perl.html
#R
#Data
#Structure
#Script
#Perl
Shruti Paniwala
@shruti
Thread
By
Shruti Paniwala
2587 days ago
Interesting PPT on cancer genomics
https:/
/
www.genome.gov/
multimedia/
slides/
genomicsinmedicine2013-2014/
helman_6-7-2013.pdf
Shruti Paniwala
@shruti
Thread
By
Shruti Paniwala
2622 days ago
BioStats with R
https:/
/
cran.r-project.org/
doc/
contrib/
Seefeld_StatsRBio.pdf
#R
#BioStats
#Example
Shruti Paniwala
@shruti
Thread
By
Shruti Paniwala
2628 days ago
Online free programming books
https:/
/
github.com/
vhf/
free-programming-books/
blob/
master/
free-programming-books.md
Shruti Paniwala
@shruti
Thread
By
Shruti Paniwala
2628 days ago
Essential perl
http:/
/
cslibrary.stanford.edu/
108/
EssentialPerl.html
Shruti Paniwala
@shruti
Thread
By
Shruti Paniwala
2636 days ago
Remove all blank lines from file. perl -i.bak -n -e "print if /\S/" ../finalSample.fa
#Perl
#Tricks
#PerlOneliner
Shruti Paniwala
@shruti
Thread
By
Shruti Paniwala
2646 days ago
Check out the OS type: $ cat /etc/*-release
#Linuxv
#OS
Shruti Paniwala
@shruti
Thread
By
Shruti Paniwala
2653 days ago
Extract values : cat seeALN.xls | grep -w "scaffold_1" to
#grep
#exact
#matching
words from file seeALN.xls
Shruti Paniwala
@shruti
Thread
By
Shruti Paniwala
2674 days ago
Fasta sequence length: awk '/^>/ {if (seqlen){print seqlen}; print ;seqlen=0;next; } { seqlen += length($0)}END{print seqlen}' file.fa
#Length
#Linux
#OneLiner
Shruti Paniwala
@shruti
Thread
By
Shruti Paniwala
2736 days ago
Extract ten lines below matched string with grep: grep -A 10 "string" filename1 ; -B for above and -C for both
#grep
#Linux
#Tricks
#Lines
#Matches
Shruti Paniwala
@shruti
Thread
By
Shruti Paniwala
2763 days ago
Slice on the fly with perl: my ($username, $real_name) = (split /:/, $str)[0, 4];
#Perl
#PerlTrick
#Split
Shruti Paniwala
@shruti
Thread
By
Shruti Paniwala
2763 days ago
Re-install perl in Ubuntu: sudo aptitude reinstall perl
#Perl
#Ubuntu
#Install
#Linux
Shruti Paniwala
@shruti
Thread
By
Shruti Paniwala
2763 days ago
Extract a fasta sequence from multifasta file: samtools faidx multitest.fa and then samtools faidx multitest.fa fasta_id > out.fa
#Samtools
#Fasta
#Extract
#Multifasta
Shruti Paniwala
@shruti
Thread
By
Shruti Paniwala
2764 days ago
Coverage R Plot
http:/
/
davetang.org/
muse/
2013/
09/
07/
creating-a-coverage-plot-in-r/
#R
#Plot
#Genome
#Image
#NGS
#BAM
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