Organizer - Badge - Bioinformatics Stack Exchange

Organizer

First retag.

Awarded 73 times.

Understanding the fasta file format and using edit distance for alignment

Awarded Feb 13 at 15:55

Cornelius Roemer

3671 silver badge13 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

2,5211 gold badge3 silver badges11 bronze badges

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

Awarded Jan 2 at 19:21

Cloudberry

2051 silver badge5 bronze badges

How can I generate ASV file from nanopore sequencing data?

Awarded Jun 27, 2022 at 17:48

Roger Vadim

3591 silver badge13 bronze badges

gtf2bed only retains gene information

Awarded Jun 15, 2022 at 23:43

Alex Reynolds

3,08510 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

1,6278 silver badges27 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

1,0454 silver badges19 bronze badges

dbSNP GRch37 Download

Awarded Aug 26, 2021 at 21:06

JRodrigoF

7055 silver badges15 bronze badges

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

Awarded Jul 9, 2021 at 11:55

O.Laprevote

4011 silver badge10 bronze badges

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

Awarded Jun 19, 2021 at 11:21

littleworth

1557 bronze badges

Removing duplicate FASTA sequences based on headers with Bash

Awarded Apr 5, 2021 at 0:10

pippo1980

7832 silver badges14 bronze badges

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

Awarded Mar 31, 2021 at 15:46

Soren

1,2739 silver badges20 bronze badges

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

Awarded Nov 2, 2020 at 20:47

jeremy

436 bronze badges

(post deleted or otherwise unavailable)

Awarded Sep 4, 2020 at 23:18

user438383

1,4341 gold badge7 silver badges20 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

1,2796 silver badges19 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

1,6581 gold badge6 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

3,3995 silver badges22 bronze badges

Marking optical or PCR duplicates with picard vs. samtools flagstat

Awarded Apr 24, 2020 at 6:09

Geraldine_VdAuwera

4303 silver badges13 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 badges10 bronze badges

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

Awarded Dec 27, 2019 at 1:00

Matteo Ferla

4,0744 silver badges19 bronze badges

(post deleted or otherwise unavailable)

Awarded Dec 18, 2019 at 2:20

dc37

1,0211 gold badge5 silver badges14 bronze badges

cooler out of memory

Awarded Dec 1, 2019 at 12:45

haci

3,6521 gold badge5 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

7215 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

6214 silver badges17 bronze badges

How do I perform a pathway related grouping of genes?

Awarded Feb 19, 2019 at 6:00

SmallChess

2,6892 gold badges15 silver badges33 bronze badges

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

Awarded Dec 16, 2018 at 17:25

M__♦

9,7633 gold badges23 silver badges44 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

3,1111 gold badge13 silver badges39 bronze badges

How to uninstall hmmpress from my conda environment?

Awarded Jul 30, 2018 at 12:50

Ammar Sabir Cheema

9317 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 badges19 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

1691 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

1,1296 silver badges26 bronze badges

Information about control data

Awarded Apr 6, 2018 at 9:34

benn

3,5517 silver badges25 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

1,65113 silver badges19 bronze badges

Database of copy number alterations in different cancer types

Awarded Feb 9, 2018 at 8:45

gc5

1,77315 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

2,57411 silver badges29 bronze badges

Obtaining all protein sequences with a particular domain architecture from Pfam

Awarded Dec 14, 2017 at 17:33

Matt Bashton

1,0496 silver badges15 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

2,65610 silver badges33 bronze badges

(post deleted or otherwise unavailable)

Awarded Aug 11, 2017 at 7:57

Chris_Rands

3,70211 silver badges29 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

7247 silver badges18 bronze badges

Reordering scaffolds according to a reference without a genetic map

Awarded Jul 11, 2017 at 7:22

AudileF

9358 silver badges25 bronze badges

using python to write bioinformatics pipelines tutorial

Awarded Jul 6, 2017 at 11:27

Dan

6023 silver badges12 bronze badges

How do I generate a color-coded tanglegram?

Awarded Jun 27, 2017 at 12:16

Konrad Rudolph

4,80512 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

6,1392 gold badges12 silver badges28 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

4,6621 gold badge17 silver badges41 bronze badges

BAM to BigWig without intermediary BedGraph

Awarded Jun 7, 2017 at 22:40

Daniel Standage

5,01013 silver badges49 bronze badges

What methods exist to calculate RNA expression profile similarity

Awarded Jun 7, 2017 at 6:20

Scott Gigante

2,1031 gold badge12 silver badges32 bronze badges

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