Organizer - Badge - Bioinformatics Stack Exchange

Organizer

First retag.

Awarded 75 times.

Python scripting with ete3 to query NCBI's Taxonomy: "sqlite3 Warning (can only execute one statement at a time)"

Awarded Oct 5 at 20:50

Harry Richman

2067 bronze badges

missed cleavages combinations generation

Awarded Jul 27 at 8:06

jay.sf

1737 bronze badges

Understanding the fasta file format and using edit distance for alignment

Awarded Feb 13 at 15:55

Cornelius Roemer

3891 silver badge14 bronze badges

Extract lines from a file based on a range of coordinates listed on a second file

Awarded Jan 11 at 7:21

Steve

3,0591 gold badge3 silver badges12 bronze badges

If fastp output is not a good measure of FASTQ correctness, what is?

Awarded Jan 2 at 19:21

Cloudberry

2722 silver badges5 bronze badges

How can I generate ASV file from nanopore sequencing data?

Awarded Jun 27, 2022 at 17:48

Roger V.

3811 silver badge15 bronze badges

gtf2bed only retains gene information

Awarded Jun 15, 2022 at 23:43

Alex Reynolds

3,12511 silver badges27 bronze badges

How to extract a subset of individuals from a .bgen file?

Awarded Dec 14, 2021 at 22:00

Giulio Centorame

1335 bronze badges

How to extract a subset of individuals from a .bgen file?

Awarded Dec 14, 2021 at 22:00

Ram RS

2,08610 silver badges28 bronze badges

The confusion of using TPM (transcripts per million)

Awarded Nov 2, 2021 at 17:30

karel

1351 silver badge8 bronze badges

Why are my Nextflow processes not executing in parallel?

Awarded Sep 4, 2021 at 20:18

user324810

1,1055 silver badges21 bronze badges

dbSNP GRch37 Download

Awarded Aug 26, 2021 at 21:06

JRodrigoF

8276 silver badges16 bronze badges

How to calculate RMSD and binding energy from the already docked ligand-receptor

Awarded Jul 9, 2021 at 11:55

O.Laprevote

4832 silver badges11 bronze badges

Best way to dock subset of protein PDB and definition of a ligand

Awarded Jun 19, 2021 at 11:21

littleworth

1559 bronze badges

Removing duplicate FASTA sequences based on headers with Bash

Awarded Apr 5, 2021 at 0:10

pippo1980

9612 silver badges14 bronze badges

Snakemake fails because it cannot create logs inside a read-only Singularity Container

Awarded Mar 31, 2021 at 15:46

Soerendip

1,29510 silver badges21 bronze badges

gmx mdrun error: "Error in user input: Invalid input values In option s"

Awarded Nov 2, 2020 at 20:47

jeremy

1436 bronze badges

(post deleted or otherwise unavailable)

Awarded Sep 4, 2020 at 23:18

user438383

1,6791 gold badge8 silver badges21 bronze badges

Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) : cannot coerce class ‘"SeqFastaAA"’ to a data.frame

Awarded May 10, 2020 at 9:55

James Hawley

1,3747 silver badges21 bronze badges

Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) : cannot coerce class ‘"SeqFastaAA"’ to a data.frame

Awarded May 9, 2020 at 20:01

StupidWolf

1,6781 gold badge7 silver badges21 bronze badges

Is it possible to go from a digital sequence to an actual nucleotide?

Awarded Apr 25, 2020 at 12:08

Maximilian Press

3,8046 silver badges22 bronze badges

Marking optical or PCR duplicates with picard vs. samtools flagstat

Awarded Apr 24, 2020 at 6:09

Geraldine_VdAuwera

4703 silver badges14 bronze badges

Protein misfolding

Awarded Apr 23, 2020 at 21:20

BalooRM

1231 silver badge5 bronze badges

Is it possible to do this in R?

Awarded Mar 10, 2020 at 15:35

Subhash C. Davar

1869 bronze badges

How to convert gff to gtf?

Awarded Jan 30, 2020 at 23:05

DavyCats

4572 silver badges11 bronze badges

How could I match atom orders between a .mol2 and a .pdb?

Awarded Dec 27, 2019 at 1:00

Matteo Ferla

4,2345 silver badges19 bronze badges

(post deleted or otherwise unavailable)

Awarded Dec 18, 2019 at 2:20

dc37

1,0211 gold badge6 silver badges14 bronze badges

cooler out of memory

Awarded Dec 1, 2019 at 12:45

haci

3,9471 gold badge6 silver badges28 bronze badges

How can I export a full alignment from IGV as an image?

Awarded Nov 4, 2019 at 16:20

Timur Shtatland

8396 silver badges12 bronze badges

How to load and split my two individual datasets when integrating datasets in Seurat?

Awarded Sep 23, 2019 at 9:05

xbello

1477 bronze badges

Find intervals that genes fall within their range

Awarded Jun 20, 2019 at 19:55

Jay Moore

1,0126 silver badges9 bronze badges

Getting data from fastq by generator

Awarded Mar 8, 2019 at 11:25

d_kennetz

6314 silver badges17 bronze badges

How do I perform a pathway related grouping of genes?

Awarded Feb 19, 2019 at 6:00

SmallChess

2,7393 gold badges18 silver badges35 bronze badges

MrBayes runs as single-core, but hangs when multi-core

Awarded Dec 16, 2018 at 17:25

M__♦

11.9k5 gold badges26 silver badges47 bronze badges

Snakemake: Cannot find first rule?

Awarded Dec 12, 2018 at 9:35

Stephopolis

1033 bronze badges

(post deleted or otherwise unavailable)

Awarded Oct 29, 2018 at 15:45

conchoecia

3,1412 gold badges13 silver badges40 bronze badges

How to uninstall hmmpress from my conda environment?

Awarded Jul 30, 2018 at 12:50

Ammar Sabir Cheema

9517 silver badges20 bronze badges

R packages for data analyses of pooled CRISPR screens

Awarded Jul 4, 2018 at 7:11

Jason Aller

1652 silver badges10 bronze badges

determining doublets in single-cell RNA-seq

Awarded May 31, 2018 at 16:35

Tom Kelly

8737 silver badges20 bronze badges

What's the best way to download data from the SRA? Is it really this slow?

Awarded May 19, 2018 at 7:15

Glorfindel

1751 gold badge2 silver badges12 bronze badges

Which are the use cases for the methods for DE in Seurat

Awarded May 13, 2018 at 8:09

Kohl Kinning

1,1496 silver badges26 bronze badges

Information about control data

Awarded Apr 6, 2018 at 9:34

benn

3,5719 silver badges27 bronze badges

Is there a Python/R package with the ability to convert an alignment and reference into a CIGAR?

Awarded Apr 4, 2018 at 18:34

ShanZhengYang

1,6811 gold badge14 silver badges19 bronze badges

Database of copy number alterations in different cancer types

Awarded Feb 9, 2018 at 8:45

gc5

1,78317 silver badges31 bronze badges

I am getting this error when running a test data set for Lyve-SET on RHEL 7. Is this an MPileup error or something else?

Awarded Dec 27, 2017 at 17:32

Bioathlete

2,57412 silver badges29 bronze badges

Obtaining all protein sequences with a particular domain architecture from Pfam

Awarded Dec 14, 2017 at 17:33

Matt Bashton

1,0596 silver badges16 bronze badges

Gene function annotation - bacterial genome

Awarded Dec 2, 2017 at 8:14

Harry Yoo

1431 silver badge5 bronze badges

How to colour multiple residues in Pymol?

Awarded Nov 16, 2017 at 18:28

quantik

2551 silver badge9 bronze badges

How to interconvert InChI and InChIKey?

Awarded Oct 16, 2017 at 14:00

Michael Kuhn

2181 silver badge4 bronze badges

Error rate setting in Canu error correction

Awarded Aug 23, 2017 at 9:26

aechchiki

2,67611 silver badges34 bronze badges

(post deleted or otherwise unavailable)

Awarded Aug 11, 2017 at 7:57

Chris_Rands

3,92812 silver badges31 bronze badges

Do any publicly available databases detail protein structure and functional domains?

Awarded Jul 27, 2017 at 9:13

Mitra

5043 silver badges11 bronze badges

Which sequence alignment tools support codon alignment?

Awarded Jul 15, 2017 at 20:48

mattm

7547 silver badges19 bronze badges

Reordering scaffolds according to a reference without a genetic map

Awarded Jul 11, 2017 at 7:22

AudileF

9558 silver badges25 bronze badges

using python to write bioinformatics pipelines tutorial

Awarded Jul 6, 2017 at 11:27

Dan

6123 silver badges12 bronze badges

How do I generate a color-coded tanglegram?

Awarded Jun 27, 2017 at 12:16

Konrad Rudolph

4,84513 silver badges44 bronze badges

Can a customized GRCh38 .gtf file be used with any of the GRCh38 released patches?

Awarded Jun 9, 2017 at 16:10

user172818

6,4852 gold badges13 silver badges29 bronze badges

How to extract RNA sequence and secondary structure restrains from a PDB file

Awarded Jun 8, 2017 at 18:31

Marcin Magnus

6763 silver badges11 bronze badges

Obtaining uniquely mapped reads from BWA mem alignment

Awarded Jun 8, 2017 at 11:41

Robert Cartaino

1009 bronze badges

How can I create my own GO association file (gaf)?

Awarded Jun 8, 2017 at 8:51

llrs

4,6931 gold badge18 silver badges42 bronze badges

2 Next