2021

• Aug 9 - Split fasta file into multiple files based on partial headers
• Aug 7 - Append file name at the end of each column for all CSV files
• Aug 6 - Add count to duplicated IDs in fasta file
• Aug 1 - Remove bases in between the sequences
• Jul 19 - Retain only unique values in the data
• Jul 19 - Replace fasta headers using regex
• Jun 24 - Determine file type without extension or with extension
• May 28 - Calculate GC content from multiline fasta with gaps in sequences
• May 25 - Split each sequence with two alleles into two sequences and convert the text to fasta
• May 24 - Replace empty values in text files with awk
• May 23 - Bar plot with unbalanced data
• May 22 - Trim fasta sequences based on a sequence in fasta file
• May 22 - Parse NCBI human reference file to a standard reference file
• May 22 - Filter sequences by stats from fasta headers
• May 20 - Merge multiple data frames in R
• May 19 - Change row font size and other properties in pheatmap
• May 18 - Identify sequences with contiguous nucleotide blocks of chosen size in multiple sequence alignment
• May 16 - Extract nucleotide and amino acid sequences from genbank and ali
• May 9 - Convert tab (tsv) file to fasta
• May 9 - Convert fasta files to tab separated file
• May 4 - Remove double extension in python
• May 1 - Split a data frame based on column names
• May 1 - Select longest sequence in a fasta with identical headers
• Apr 21 - Make fasta from Blast results
• Apr 12 - Locate if a base is present at the start of sequences in a list
• Apr 10 - Extract sequences(lines) from multiline, multisequence fasta
• Apr 4 - Extract genes and corresponsing transcripts with more than one 3' UTRs from a gtf
• Apr 4 - Duplicate a data frame
• Mar 28 - Format VEP text output with Miller
• Mar 24 - Replace separator, without replacing separator in quotes
• Mar 24 - Extract reads between primers including one side primer only
• Mar 23 - Break multifasta into multiple files with awk
• Jan 17 - Manipulate fasta file with AWK
• Jan 16 - Column operations using dplyr and tidyr

2020

• Dec 23 - Change row font color in pheatmap conditionally
• Dec 21 - A small tutorial on ggplot2
• Dec 19 - Serial and Parallel writing of Individual fasta files in R
• Dec 17 - Manipulate fasta headers using back referencing
• Nov 1 - How to install VEP on focal
• Oct 29 - Generate substrings in python
• Oct 28 - Generate overlapping strings
• Oct 21 - Average biological replicates
• Oct 16 - Remove header information after space in fasta
• Oct 12 - Format fasta headers
• Oct 5 - Percentage pie chart with python 3
• Oct 3 - Percentage pie chart in R
• Sep 3 - Batch rename files from a file
• Sep 3 - One liners in bioinformatics (ever updating)
• Sep 3 - Remove named columns from several files
• Sep 3 - Reorganize and rename fasta
• Aug 26 - Clean data with altenating match pair columns
• Aug 26 - Clean two column data using tidyr
• Aug 15 - Annotate text file with dbSNP reference
• Aug 15 - Tabix error and bcftools failure in handling unsorted vcf
• Aug 15 - Annotate text file with dbSNP VCF
• Aug 12 - Run multiple Anova tests in parallel
• Aug 9 - Run anova tests in parallel in R
• Aug 1 - Uncount, multiple replacement and grouping using dplyr
• Aug 1 - Uncount function in R
• Jul 27 - Retain sequences based on partial match of headers
• Jul 27 - Partial renaming of fasta headers
• Jul 11 - Control grouped barcharts in ggplot
• Jul 11 - Convert sff files to fastq file
• Jul 7 - Simple row wise ttest function and extract the p value
• May 31 - Row wise filtering for alphanumeric strings in R
• May 24 - Conditional filtering of columns with AWK
• May 12 - Add vertical lines with plotly
• Apr 30 - Compare all or few columns against a single column or value in a data frame
• Feb 19 - Merge fastq files from multiple directories with snakemake
• Jan 27 - glimma error: Second argument should contain the first.

2019

• Mar 4 - install fastq validator

2018

• Nov 11 - De duplicate data frame
• Sep 2 - Sam to fastq conversion and tag extraction
• Sep 1 - Multiline pattern search using R, grep, pcregrep and awk
• Aug 9 - Parse PDF tabular data in R
• Aug 5 - Plot numbers in R
• Aug 4 - Zero length assertions in bash and python 3
• Jul 20 - Zero length assertion example in R
• Jul 20 - Replace wobble base with purine (R) and pyrimidine (Y) symbol in python
• Jul 16 - Gene clustering and extract clusters, genes and samples of interest
• Jul 16 - Add sample number to venn diagram
• Jul 13 - Extract columns using R and shell from xls files
• Jul 6 - Add increment numbers to fasta headers using nl
• Jul 6 - Lookaround example in bash
• Jul 6 - Sort columns individually per variable
• Jul 4 - Plotting ggpairs list, saving and faceting
• Jul 3 - Convert tab separated file to fasta
• Jul 3 - Parallel download genomic data with GNU-Parallel
• Jun 28 - Getting rs IDs given coordinates in R and shell
• Jun 26 - Group by and column wise statistics in Shell, R and Python 3
• Jun 25 - Gene expression plotting using Lollipop plots for two conditions in R
• Jun 17 - Convert PMIDs to PMCIDs using shell and python
• Jun 12 - Split fasta sequence files by an unique base
• Jun 12 - Replace column names in R from another data frame
• Jun 12 - Replace gene symbols with gene IDs in data frame
• Jun 9 - Faceting gene expression per variable and connecting by means using ggplot
• Jun 8 - Step by step faceting box plots using ggplot2
• Jun 6 - Extract KEGG pathways and IDs using gene symbols
• Jun 2 - Average triplicate columns in R
• May 30 - Facet gene expression time series in ggplot2
• May 25 - Convert 3 letter HGVS pSynax to 1 letter pSyntax
• May 20 - Salmon reference formatting
• May 19 - Salmon-DESEQ2 and Salmon-Wasabi-Sleuth pipe line with Snakemake
• May 19 - Pandas multijoin dataframes with dots in column names
• May 14 - back referencing and string manipulation with GNU-Parallel
• May 14 - concatenate two columns in R
• May 12 - Volcano plot with ggplot2 and basic plotting
• May 9 - Manipulate fasta headers and GTF sequence IDs with awk
• May 7 - ggplot and alternate shading with geom_rect
• May 5 - inner and outer join or symmetric difference with pandas
• Apr 28 - Plotting time series experiments with ggplot2 (bar and line plots)
• Apr 28 - Collapse rows using gather and spread functions
• Apr 23 - Split columns in R data frame
• Apr 21 - Extract matching peptides/short sequences with mismatches
• Apr 20 - coverage calculation
• Apr 11 - Random fasta sequence generation
• Mar 13 - Replace fasta headers with file name
• Feb 27 - Controlling IGV locally from shell and browser
• Jan 30 - RNAseq workflow using snakemake
• Jan 20 - hisat2, conda, bioconda and windows 10

2017

• Dec 15 - Identify multi exonic genes from gtf
• Dec 15 - Split a gtf file by chromosome
• Dec 15 - Highlight points in a box plot
• Dec 13 - PCA plot with read counts using ggplot2
• Dec 4 - Extract sequences and sequence headers into individual files from fasta file
• Dec 1 - Nucleotide (base) frequency per read and per position using bioconductor
• Nov 29 - Heat map with RNAseq Featurecounts output
• Nov 24 - RNA seq analysis - FeatureCounts and DESeq2 workflow
• Nov 23 - Extract clinical signifiance and variant effect of dbSNP variants using biomart
• Nov 19 - Parse KEGG output with miller
• Nov 9 - Join dataframes by range in R
• Nov 7 - Extract KEGG pathways using KEGG IDs using bash and R
• Oct 17 - Uninstall perl modules when make uninstall fails
• Oct 4 - Replace gene IDs in UCSC gtf
• Oct 2 - RNAseq Ballgown analysis
• Oct 1 - RNAseq data analysis- Tuxedo new protocol
• Sep 19 - FastQ screen and NGS data analysis
• Sep 19 - GNU parallel and NGS data organization
• Sep 17 - Handling samflags in R
• Sep 14 - Manipulate fasta header with sed, awk and R
• Sep 13 - Replace fasta headers from a file
• Sep 13 - Split and melt columns in R
• Aug 5 - Find common genes between two gene lists
• Jul 31 - Remove both rows and columns with NA values in R
• Jul 31 - Filter fasta sequences by length
• Jun 21 - Fastq manipulation

2016

• Nov 3 - Write list to xlsx in R
• Oct 4 - Extract sequences from fasta file
• Sep 24 - Connecting box plots by median in 3 different plotting methods in R
• Jun 8 - Generate random amino acid sequences using python/biopython
• Jun 7 - Generate random DNA elements using python/biopython
• May 21 - Plotting variants per chromosome using ggplot2
• May 16 - VCF tricks
• Apr 18 - Plot interactome data in R
• Apr 18 - qPCR, ddCt and tab separated values

2015

• Oct 10 - RNA seq variant calling best practice pipeline
• Sep 11 - Transcriptomics - Microarray data analysis
• Sep 10 - Download and use microarray files from GEO in R
• Sep 7 - Convert VCF #CHROM column from hgxx format to b3x format
• Sep 5 - RNAseq data analysis and Tuxedo workflow
• Aug 31 - RNA seq data analysis - Tophat, HTseq and DESeq 2 analysis
• Aug 20 - Combine multiple data frames into a single dataframe in R
• Aug 16 - Transcriptomics: RNA seq and 3'IVT and exon arrays
• Jul 22 - Variant calling in RNA seq and Bpipe
• Jul 21 - Extract sequences from fasta
• Jul 14 - Natural sort chromosome levels in R- method 2
• Jul 14 - Fetch and natural sort cytoband info from UCSC
• Jul 13 - Parsing Clinvar VCF using dplyr and vcflib
• Jul 2 - Simulate nucleotide and amino acid sequences with R- Part 2
• Jul 1 - Simulate nucleotide and amino acid sequences with R- Part 1
• Jun 6 - Use mouse4302.db object in Bioconductor
• Jun 6 - Exporting Ideogram information from UCSC table browser
• Jun 5 - natural sort chromosome number in R - method 1
• May 29 - plot and highlight genes of interest in R
• May 25 - Plotting two Y-axes in R
• May 18 - Install BCFtools, VCFlib and Samtools

2014

• Jul 25 - Convert bam files to cram files
• Jul 23 - Gene expression and Circos plot
• Jul 21 - Gene expression and treemaps
• Jul 18 - Fetch chromosome sizes from UCSC in linux
• Jul 18 - sort and merge fasta files by chromosome number
• Jul 17 - Calculate coverage from bam files using IGV tools
• Jul 17 - using Biomart in R
• Jul 15 - Parse VCF 1
• Jul 14 - Parse fasta file
• Jul 13 - Blog reloaded

2010

• Dec 30 - flashing buffalo WHR-HP-G54 router
• Nov 26 - Drupal on maverick
• Nov 24 - zabbix with lighttpd on maverick (ubuntu)
• Nov 10 - Delete persistent flash cookies in windows and linux
• Nov 9 - How to upgrade from iso in ubuntu
• Nov 8 - Installing Care2x on Ubuntu
• Nov 8 - Share thunderbird mail accounts between windows and Linux