Excavator - Badge - Bioinformatics Stack Exchange

Excavator

Edit first post that was inactive for 6 months.

Awarded 55 times.

UPGMA computation

Awarded Sep 14 at 4:10

Harry Richman

1315 bronze badges

Converting Ensembl Gene IDs to Entrez Gene IDs through biomart

Awarded Sep 8 at 4:41

justinian482

3351 silver badge12 bronze badges

What Ensembl genome version should I use for alignments? (e.g. toplevel.fa vs. primary_assembly.fa)

Awarded Aug 12 at 4:32

ATpoint

9039 bronze badges

How to filter a SAM file by a bed file?

Awarded May 9 at 5:05

Amar

1436 bronze badges

Server for finding kmers in set of sequences

Awarded Apr 19 at 4:30

Roger Vadim

3811 silver badge15 bronze badges

Correspondence of SARS-CoV-2 annotations (Nextstrain clades - Pango lineages)

Awarded Feb 14 at 6:41

Cornelius Roemer

3871 silver badge14 bronze badges

Fix dash/empty ALT alleles for deletions in VCF

Awarded Jan 26 at 6:11

JNR

32 bronze badges

Protein-Ligand in PDB

Awarded Jan 13 at 6:20

pippo1980

8272 silver badges14 bronze badges

How can I find the chromosomal location of a list of genes?

Awarded Nov 17, 2022 at 4:15

JRodrigoF

7155 silver badges15 bronze badges

I am trying to run nab to create the pdb file but it isn`t working (AMBER)

Awarded Aug 16, 2022 at 4:27

Ram RS

1,99310 silver badges28 bronze badges

Efficiently aligning a lot of reads on the same small reference sequence

Awarded Aug 10, 2022 at 7:26

pedrosaurio

1033 bronze badges

Convert .smp downloaded from NCBI CDD into HMM(.hmm) file [closed]

Awarded Jul 22, 2022 at 4:42

Shruti Kapil

32 bronze badges

Help with performing PCA analysis on data from 3 different datasets of normalized counts data for RNA-seq experiment

Awarded Jul 19, 2022 at 4:08

James Hawley

1,3647 silver badges20 bronze badges

STAR aligner multiple fastq files

Awarded Dec 10, 2021 at 5:19

Scot

7474 silver badges8 bronze badges

Generate an appropriate output from DNaSP6 to Arlequin program

Awarded Dec 5, 2021 at 5:48

tyersome

1035 bronze badges

How to import a large amount of .bed, .gff, .vcf, .paf, .sam files into an SQL database?

Awarded Nov 11, 2021 at 4:03

Dan Bolser

4702 silver badges10 bronze badges

insert size pre and post trimming

Awarded Sep 3, 2021 at 6:41

Timur Shtatland

7555 silver badges12 bronze badges

How to create a .bed file from .fasta?

Awarded Sep 3, 2021 at 6:41

0x90

1,4279 silver badges17 bronze badges

Converting a VCF into a FASTA given a reference with Python, R

Awarded Jul 4, 2021 at 5:35

TimD1

2821 silver badge8 bronze badges

Minimizing particle-flow grid mapping time of a protein surface using spherical-coordinates and differentiation encoding [closed]

Awarded May 12, 2021 at 4:18

LMR

32 bronze badges

Where did the BIND website go?

Awarded May 8, 2021 at 4:15

user438383

1,6211 gold badge7 silver badges21 bronze badges

How I know which gene is a good predictor in this neural network or not?

Awarded Apr 14, 2021 at 8:47

maciejwww

2151 silver badge11 bronze badges

Proper use of BWA MEM on multiplexed GBS sample

Awarded Feb 16, 2021 at 4:10

Maximilian Press

3,6495 silver badges22 bronze badges

Difference between CPM and TPM and which one for downstream analysis?

Awarded Jan 7, 2021 at 4:58

Kevin L. Keys

1056 bronze badges

Selecting sites from VCF which have an alt AD > 10

Awarded Dec 4, 2020 at 4:10

Matt Bashton

1,0596 silver badges16 bronze badges

Interpretion of my coronavirus 2019-nCov, Wuhan, China BLAST tree?

Awarded Dec 2, 2020 at 4:31

Alexlok

3071 silver badge8 bronze badges

Is it wise to use RepeatMasker on prokaryotes?

Awarded Sep 8, 2020 at 4:04

ahua217

33 bronze badges

When running ChIPQC bioconductor package after peak calling, should I use sorted BAM files or unsorted BAM files?

Awarded Sep 3, 2020 at 21:56

StupidWolf

1,6781 gold badge7 silver badges21 bronze badges

Obtaining identifier from plot of sequence GC%

Awarded Aug 8, 2020 at 5:32

RockPaperLz- Mask it or Casket

1035 bronze badges

Fix dash/empty ALT alleles for deletions in VCF

Awarded Jul 10, 2020 at 4:46

jz314

52 bronze badges

ATAC-seq peak annotation and downstream analysis

Awarded Jun 18, 2020 at 5:10

karel

1351 silver badge8 bronze badges

Picard validation error regarding bin field of BAM file

Awarded Apr 24, 2020 at 20:15

Geraldine_VdAuwera

4503 silver badges13 bronze badges

Can structural - equation modeling be used in Bioinformatics?

Awarded Mar 13, 2020 at 4:45

Subhash C. Davar

1869 bronze badges

sva for RNA-Seq data without known phenotype

Awarded Feb 4, 2020 at 4:05

haci

3,8921 gold badge5 silver badges28 bronze badges

Script to allow gene set enrichment analysis of 10x genomics data in R

Awarded Jan 11, 2020 at 4:25

Gildas

1033 bronze badges

(post deleted or otherwise unavailable)

Awarded Jan 8, 2020 at 5:00

Kohl Kinning

1,1396 silver badges26 bronze badges

Proof of Breakpoint Reversal Sorting Approximation Algorithm

Awarded Nov 12, 2019 at 4:50

Eric Leung

1551 silver badge5 bronze badges

What's the most efficient file format for the storage of DNA sequences?

Awarded Oct 12, 2019 at 4:15

ashima panjwani

31 silver badge3 bronze badges

Converting Gene Symbol to Ensembl ID in R

Awarded Sep 26, 2019 at 4:40

kritisen

32 bronze badges

What are 2D reads in the Oxford MinIon?

Awarded Jun 1, 2019 at 7:00

Mark Amery

2672 silver badges13 bronze badges

How to convert fasta file to tab delimited file

Awarded May 24, 2019 at 4:05

terdon♦

9,4223 gold badges21 silver badges45 bronze badges

How can we distinguish between true zero and dropout-zero counts in single-cell RNA-seq?

Awarded May 13, 2019 at 5:05

Tapper

676 bronze badges

Coverage calculation: long reads (RNA-seq)

Awarded Apr 16, 2019 at 4:15

Glorfindel

1751 gold badge2 silver badges12 bronze badges

Mapping a list of cells in seurat featureplot

Awarded Apr 11, 2019 at 5:00

Gilad Green

1357 bronze badges

Simplest way to work out structural variant type?

Awarded Mar 29, 2019 at 4:00

Christopher Bottoms

1687 bronze badges

Select top 100 genes ranked by variance in read counts

Awarded Jan 31, 2019 at 4:10

Daniel Standage

5,06015 silver badges50 bronze badges

What to use to edit RNA alignments?

Awarded Dec 31, 2018 at 6:20

Bioathlete

2,57412 silver badges29 bronze badges

Is there a standard way to clean a PDB file and re-number its residues?

Awarded Dec 16, 2018 at 12:35

M__♦

11.2k4 gold badges26 silver badges46 bronze badges

(post deleted or otherwise unavailable)

Awarded Oct 17, 2018 at 15:00

Kamil S Jaron

5,4971 gold badge23 silver badges59 bronze badges

Annovar index out of date

Awarded May 22, 2018 at 5:43

Jason Aller

1652 silver badges10 bronze badges

Difference between BWA-backtrack and BWA-MEM

Awarded Apr 10, 2018 at 8:36

aechchiki

2,65611 silver badges34 bronze badges

Influence of pH on protein peptide mass

Awarded Feb 23, 2018 at 4:38

Peter Mortensen

1314 bronze badges

Filtering imputed GWAS SNPs based on a MAF difference of 10%

Awarded Jan 17, 2018 at 5:31

Devon Ryan

19.5k2 gold badges29 silver badges60 bronze badges

Accuracy of the original human DNA datasets sequenced by Human Genome Project?

Awarded Dec 29, 2017 at 1:40

gringer♦

13.5k5 gold badges22 silver badges78 bronze badges

What methods exist to calculate RNA expression profile similarity

Awarded Dec 8, 2017 at 4:45

llrs

4,6821 gold badge18 silver badges42 bronze badges