Waldeyr Mendes Cordeiro da Silva waldeyr

## Bioinformatics tricks
# Just some small codes to help myself and others...

## genome_oneliners.md

      
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                darencard
                / genome_oneliners.md
            
            
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              September 25, 2025 19:01
            
              
                Quick one-liner commands that are useful for genomics
              
          
    Useful Genomics Oneliners

The following commands sometimes require non-standard software like bioawk and seqtk.
rename scaffold headers with sequential numbers and lengths ("scaffold-N ")
bioawk -c fastx '{ print ">scaffold-" ++i" "length($seq)"\n"$seq }' < genome.fasta > new_genome.fasta
make association table of old and renamed scaffold names after above renaming command

  
## neo4j_cypher_cheatsheet.md

      
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                DaniSancas
                / neo4j_cypher_cheatsheet.md
            
            
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              June 14, 2016 23:52
            
              
                Neo4j's Cypher queries cheatsheet
              
          
    Neo4j Tutorial

Fundamentals

Store any kind of data using the following graph concepts:

Node: Graph data records
Relationship: Connect nodes (has direction and a type)
Property: Stores data in key-value pair in nodes and relationships
Label: Groups nodes and relationships (optional)


## counts_to_tpm.R
#' Convert counts to transcripts per million (TPM).
#'
#' Convert a numeric matrix of features (rows) and conditions (columns) with
#' raw feature counts to transcripts per million.
#'
#'    Lior Pachter. Models for transcript quantification from RNA-Seq.
#'    arXiv:1104.3889v2
#'
#'    Wagner, et al. Measurement of mRNA abundance using RNA-seq data:
#'    RPKM measure is inconsistent among samples. Theory Biosci. 24 July 2012.

## countries_codes_and_coordinates.csv

          
            Country
            Alpha-2 code
            Alpha-3 code
            Numeric code
            Latitude (average)
            Longitude (average)

            
              Afghanistan
              AF
              AFG
              4
              33
              65

            
              Åland Islands
              AX
              ALA
              248
              60.116667
              19.9

            
              Albania
              AL
              ALB
              8
              41
              20

            
              Algeria
              DZ
              DZA
              12
              28
              3

            
              American Samoa
              AS
              ASM
              16
              -14.3333
              -170

            
              Andorra
              AD
              AND
              20
              42.5
              1.6

            
              Angola
              AO
              AGO
              24
              -12.5
              18.5

            
              Anguilla
              AI
              AIA
              660
              18.25
              -63.1667

            
              Antarctica
              AQ
              ATA
              10
              -90
              0
	#' Convert counts to transcripts per million (TPM).
	#'
	#' Convert a numeric matrix of features (rows) and conditions (columns) with
	#' raw feature counts to transcripts per million.
	#'
	#' Lior Pachter. Models for transcript quantification from RNA-Seq.
	#' arXiv:1104.3889v2
	#'
	#' Wagner, et al. Measurement of mRNA abundance using RNA-seq data:
	#' RPKM measure is inconsistent among samples. Theory Biosci. 24 July 2012.
Country	Alpha-2 code	Alpha-3 code	Numeric code	Latitude (average)	Longitude (average)
Afghanistan	AF	AFG	4	33	65
Åland Islands	AX	ALA	248	60.116667	19.9
Albania	AL	ALB	8	41	20
Algeria	DZ	DZA	12	28	3
American Samoa	AS	ASM	16	-14.3333	-170
Andorra	AD	AND	20	42.5	1.6
Angola	AO	AGO	24	-12.5	18.5
Anguilla	AI	AIA	660	18.25	-63.1667
Antarctica	AQ	ATA	10	-90	0