NCBI-Hackathons EDirectCookbook issues

NCBI-Hackathons / EDirectCookbook

MIT License

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issues

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How to print an empty field if no data is found?

#63 panosioannidis opened 1 year ago
0
How to merge data from two different databases into one output file?

#62 panosioannidis closed 1 year ago
3
Get coding sequences for a gene id

#61 snk5040 opened 1 year ago
2
Retrieve all metadata from edirect that is accessible from SRArunTable

#60 kray02 opened 1 year ago
0
Download Symbol via EFetch

#59 mapauley opened 2 years ago
9
Downloading FASTA Records with GI Number via efetch?

#58 mapauley opened 2 years ago
2
Download 1,000 Random Human RefSeq Transcripts

#57 mapauley opened 2 years ago
2
getting the fastq reads from accession ids

#56 Jigyasa3 opened 2 years ago
1
Retrieve bioproject IDs and SRA IDs from PMIDs?

#55 Jigyasa3 opened 2 years ago
3
Overall design

#54 xexpanderx opened 3 years ago
0
Citation List

#53 smartdance opened 3 years ago
0
curl: (60) SSL certificate problem: unable to get local issuer certificate

#52 ShuqingL opened 3 years ago
0
Adding a recipe to get all assemblies associated with a bioproject

#51 linsalrob opened 4 years ago
1
Retrieve Bioproject IDs and related SRAs within given timerange

#50 tbmz closed 4 years ago
2
The importance of adding < /dev/null with while loops

#49 nickp60 opened 4 years ago
0
Get Transcription Factors ChiP-seq experiments

#48 Fnyasimi opened 4 years ago
0
get nucleotide sequence by gene ID

#47 plasmid02 opened 4 years ago
12
Get entries that have specific keyword in the tag "Isolation source"

#46 jeagull opened 5 years ago
0
The efetch command reported BioSamples’ Attributes completely different from those displayed at the NCBI website

#45 lauraht opened 5 years ago
2
The “-if” and “-unless” statements in xtract did not seem to work for me when extracting Attributes in BioSample

#44 lauraht opened 5 years ago
3
How to use xtract to get <name value> pairs of all the attributes?

#43 lauraht closed 5 years ago
0
API Keys

#42 linsalrob opened 5 years ago
1
Software Version

#41 linsalrob opened 5 years ago
1
Extracting Pubmed ID (PMID) for a list of refseq accession number

#40 tauqeer9 opened 5 years ago
2
Get publication counts per gene per year

#39 sanyalab opened 5 years ago
6
HTML code in Pubmed "title" field

#38 cmonnom opened 5 years ago
0
EDirect pulling [crdt] against [entrez] to get all PMID's for 2017 where they don't match

#37 tomlaheyh opened 5 years ago
0
EDirect installation requires LWP::Protocol::https

#36 linsalrob opened 6 years ago
1
added formatting

#35 lwagnerdc closed 6 years ago
0
added recipe for retrieving pmc citations of pmid

#34 lwagnerdc closed 6 years ago
0
geoprofiles data format

#33 rbutleriii opened 6 years ago
0
Get DNA Sequences for a bacterial protein with a given name

#32 MoamenElmassry opened 6 years ago
0
How to limit esearch results retmax or similar?

#31 cmdcolin opened 6 years ago
4
Containerize / homebrew installation

#30 tom-dyar opened 6 years ago
0
Get all Eukaryote mitochondrial markers

#29 DCGenomics opened 6 years ago
1
Runs from another Run ID

#28 linsalrob closed 6 years ago
0
using xtract to get SRA ids and BioProject ids

#27 pedrorvc opened 6 years ago
2
Formatting and missing value issue in xtract metadata from bioproject

#26 ghost closed 6 years ago
1
Get child nodes from NCBI taxonomy

#25 DCGenomics opened 6 years ago
4
Added first author/equal contrib script

#24 mikeadavidson closed 6 years ago
0
Added two scripts

#23 mikeadavidson closed 6 years ago
0
Extract all MeSH Headings from a given PMID

#22 DCGenomics closed 6 years ago
1
Added taxon to RefSeq genome FASTA files example

#21 ucpete opened 7 years ago
0
Adding how to get the size of the SRA datasets in bp

#20 linsalrob closed 7 years ago
0
assembly field SB

#19 linsalrob opened 7 years ago
2
Get filesizes for a list of SRA files

#18 tobsecret opened 7 years ago
4
extract sequence ranges from bacterial genomes

#17 DCGenomics opened 7 years ago
5
Extract biological regions from an NCBI .gff3 file

#16 DCGenomics opened 7 years ago
1
How to find amino acid changes from SNPs?

#15 anmolv07 opened 7 years ago
2
Go from rs# to Gene Ontology

#14 cbauer82 opened 7 years ago
3