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Showing top results for tag: coordinates • reset
1
vote
2
replies
187
views
Search PDB-format files for residue contacts
pdb structure coordinates
updated 4 weeks ago by ▴ 170 • written 5 weeks ago by ▴ 10
205
votes
32
replies
117k
views
24 follow
Tool: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
genome coordinates conversion liftover ensembl Tool
updated 7 weeks ago by ▴ 30 • written 8.6 years ago by 19k
2
votes
5
replies
3.6k
views
Adding Introns To Gff3 Format?
coordinates gff3 conversion
updated 10 weeks ago by 34k • written 8.6 years ago by ▴ 870
0
votes
0
replies
229
views
liftover results usage: input bed file and output bed file have different rows, how can I link coordinates between input and output files?
unmapped liftover coordinates relationship
3 months ago by wangjinpeng0225 ▴ 30
3
votes
4
replies
707
views
Which R function can be used for intersection of genomic coordinates from one file and check if the coordinates are within a specific range?
coordinates R Genomic
10 weeks ago by bioinfo89 ▴ 40
0
votes
0
replies
117
views
Intersecting multiple bed files with reporting the number of base pairs of overlap between the features - Pybedtools
Pybedtools Coordinates Python Bedtools
3 months ago by BioICoder ▴ 40
1
vote
4
replies
326
views
common coordinates from 10 files
coordinates common
3 months ago by K • 0
0
votes
4
replies
302
views
Window Length to Genomic Coordinates
coordinates Gene
updated 4 months ago by 34k • written 4 months ago by ▴ 70
2
votes
4
replies
288
views
how to find homology in DNA regios
coordinates homology sequences blast
4 months ago by Lila M ★ 1.1k
0
votes
5
replies
322
views
Merging two linux files based on same rows
rsID coordinates plinkfile Merge
updated 4 months ago by 107k • written 4 months ago by ▴ 50
6
votes
5
replies
331
views
6 follow
Remove 2nd colon and rest of the values in a dataframe using R/ Unix
coordinates SNP Unix R
updated 5 months ago by 10k • written 5 months ago by ▴ 50
0
votes
0
replies
156
views
Find genomic coordinates for exons in historical transcripts
genome exon human coordinates
5 months ago by raptly61549 • 0
0
votes
1
reply
277
views
Method detecting surface / bounday Carbon-alpha (or sidechains) atoms of PDB 3d coordinates / points
pdb amino acid surface coordinates protein
updated 7 months ago by ★ 13k • written 8 months ago by • 0
239
votes
32
replies
72k
views
22 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates tutorial Tutorial
updated 7 months ago by ▴ 20 • written 7.9 years ago by 19k
2
votes
4
replies
563
views
Get gene promoter coordinates
gene promoter coordinates hg38
10 months ago by sabin ▴ 40
12
votes
10
replies
2.2k
views
6 follow
Create Chain File for Converting Genome Coordinates
assembly genome liftover coordinates alignment
updated 11 months ago by 8.0k • written 2.2 years ago by ▴ 50
3
votes
5
replies
419
views
Get rs ids using chromsome coordinates
rs id Chromosome Coordinates Hg38
updated 12 months ago by 20 • written 13 months ago by ▴ 70
0
votes
1
reply
881
views
EPIC methylation manifest GRch38 query
methylation coordinates EPIC bedgraph CpG
15 months ago by prasundutta87 ▴ 570
1
vote
1
reply
571
views
determine exon number from variant genomic coordinates
exon coordinates variant human exome
updated 17 months ago by ★ 1.7k • written 17 months ago by ▴ 170
5
votes
3
replies
5.2k
views
Easy Way To Map Cds Coordinates To Genomic Coordinates
cds mapping gff bed coordinates
updated 20 months ago by ★ 8.8k • written 10.5 years ago by ▴ 100
0
votes
0
replies
340
views
conversion of genomic variant to coding variant to protein variant
SNP conversion variant coordinates
21 months ago by justinms ▴ 10
0
votes
2
replies
548
views
index tabulate file to get chrom, pos, ref, alt
tabix coordinates variants indexing
updated 21 months ago by 138k • written 21 months ago by ▴ 20
0
votes
2
replies
515
views
Retrieve base position/coordinates due to AA position on a protein
base position coordinates aminoacid
2.3 years ago by cocchi.e89 ▴ 170
1
vote
8
replies
572
views
UCSC different exome sets per each gene
ucsc exomes gene coordinates
updated 2.3 years ago by ▴ 510 • written 2.3 years ago by ▴ 170
1
vote
1
reply
2.0k
views
genetic coordinates hg19/GRCh37 latest version
refseq gene coordinates hg19 grch37
2.6 years ago by cocchi.e89 ▴ 170
1
vote
1
reply
2.6k
views
Map Uniprot On Genomic Coordinates (Eg. Hg19)
coordinates mapping uniprot
updated 2.7 years ago by 20 • written 9.4 years ago by ▴ 10
17
votes
3
replies
12k
views
Getting Sequence Based On Chromosome No And Coordinates From Whole Genome Fasta File
sequence coordinates tool
updated 2.9 years ago by 20 • written 9.5 years ago by ▴ 20
0
votes
1
reply
1.1k
views
How to divide a chromosome into arms and center?
chromsome arm center bed coordinates
2.9 years ago by Zee_S ▴ 60
11
votes
14
replies
1.8k
views
Extracting snps from a range of coordinates
vcf SUB-SET SNP gene coordinates
updated 3.0 years ago by ★ 1.0k • written 3.0 years ago by ▴ 70
19
votes
11
replies
8.3k
views
8 follow
How To Extract Just The Coordinate Values From A Pdb File Converted To A Text File, In Java Only?
coordinates java pdb parsing structure
updated 3.0 years ago by 34k • written 11.2 years ago by ▴ 30
20
votes
7
replies
13k
views
How Do I Get The Gene Names From The Chromosome Locations In A Wig File
wiggle ucsc coordinates galaxy
updated 3.1 years ago by 34k • written 11.4 years ago by ★ 1.4k
4
votes
5
replies
873
views
Get variant position knowing the gene name, base change, and NM#
gene variant genome coordinates
updated 3.3 years ago by ▴ 450 • written 3.3 years ago by ▴ 10
0
votes
1
reply
1.8k
views
Retrieve genomic coordinates (locus start, locus end) from blastn hits?
blastn locus coordinates reciprocal best hits
updated 3.4 years ago by 20 • written 3.6 years ago by • 0
0
votes
1
reply
1.4k
views
Blast subject coordinates
Blast Subject Coordinates
updated 3.4 years ago by 34k • written 3.4 years ago by ▴ 40
0
votes
1
reply
840
views
fantom5 enhancers GRCh38
enhancers genomics coordinates r fantom5
3.4 years ago by Pin.Bioinf ▴ 300
0
votes
1
reply
763
views
how to get intergene coordinates for a single chromosome?
bedtools intersect intergene coordinates
3.4 years ago by Zee_S ▴ 60
0
votes
5
replies
2.8k
views
Finding hg19 coordinates for primers to make BED file
primers coordinates hg19
updated 3.4 years ago by ▴ 40 • written 5.7 years ago by ▴ 10
9
votes
10
replies
9.8k
views
9 follow
Is There An Easy Way Of Getting Gene Symbols From Genomic Coordinates?
gene coordinates
updated 3.5 years ago by ▴ 560 • written 8.2 years ago by ▴ 20
31
votes
19
replies
17k
views
9 follow
Converting Ensembl Gene Ids To Hgnc Gene Name / Coordinates
ensembl ucsc genome mapping coordinates
updated 3.7 years ago by ▴ 10 • written 9.9 years ago by ★ 3.4k
1
vote
2
replies
2.9k
views
Mutation Taster Gdna Coordinates
mutation coordinates
updated 3.9 years ago by 20 • written 9.0 years ago by • 0
9
votes
4
replies
928
views
Data Mining from my Genomic Coordinates
ngs vcf database sql coordinates
updated 3.9 years ago by 77k • written 3.9 years ago by ★ 1.4k
36
votes
14
replies
22k
views
7 follow
Exon Coordinates Of Hg19 Genome Download
exon coordinates hg human
updated 5 months ago by • 0 • written 10.5 years ago by ▴ 150
2
votes
2
replies
1.5k
views
[hg19] Reading genes with CCDS
GRCH37 hg19 CCDS coordinates
updated 4.0 years ago by ★ 1.6k • written 4.0 years ago by ▴ 80
2
votes
1
reply
2.5k
views
Can One Use The Ensembl Api To Retrieve Multiple Alignment Between The 46 Vertebrate Species
coordinates alignment ensembl
updated 4.3 years ago by 20 • written 9.2 years ago by ▴ 40
21
votes
19
replies
14k
views
8 follow
How To Extract Just The Coordinate Values From A Pdb File, Using Perl Only?
pdb protein coordinates parsing perl
updated 4.4 years ago by 20 • written 10.5 years ago by ▴ 20
11
votes
3
replies
1.9k
views
Construct a gene arrow map to show the gene features
gene map Coordinates Annotation
updated 4.5 years ago by 138k • written 4.5 years ago by ▴ 40
1
vote
1
reply
2.1k
views
Variant coordinates in dbSNP VCF
dbSNP VCF coordinates indel RSPOS
4.7 years ago by wjastle ▴ 10
0
votes
0
replies
1.2k
views
MCS-R2 (encode HS-40) hg19 genomic coordinates
coordinates DNase ENCODE Assembly
4.7 years ago by eurioste ▴ 20
19
votes
16
replies
9.1k
views
7 follow
Get Snp Position From A Python Interface.
python snp tabix coordinates
updated 4.9 years ago by ▴ 80 • written 8.8 years ago by ▴ 630
1
vote
0
replies
1.4k
views
extract genomic sequence based on transcripts
genome transcripts FASTA extract coordinates
updated 5.3 years ago by 34k • written 5.3 years ago by ▴ 50
50 results • Page 1 of 1
Recent Votes
Answer: How can I extract upstream regions in fasta for all blastx hits locally performe
C: What Are The Most Common Stupid Mistakes In Bioinformatics?
Comment: Beginner problem: installed python3.7.12 but py_available() return FALSE
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A: ATAC-seq sample normalization (quantil normalization)
C: Help to analyze DEseq-MA-Plot.
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Recent Replies
Comment: Automatic Outlier Detection for RNA-seq data by Kevin Blighe 77k
There is actually, well, a sort of citation off the top of my head. Please see the PLINK documentation (section '*Outlier detection diagnos…
Answer: Batch effects by swbarnes2 11k
It's always safest to get raw data and normalize it yourself. If one dataset is control, and the other is not, there is no magic way to …
Comment: GREP from multiFasta file and keep headers by Pierre Lindenbaum 138k
your command line with `grep` **implies** that each record in your fasta file takes only two line (?). One line for the header, and one lin…
Answer: In what way should cellranger count be performed , when there are multiple runs by swbarnes2 11k
If you did **one** library prep and ran that one library prep multiple times, it is probably easiest to combine the fastqs (make sure to gi…
Comment: Splice aware vs splice unaware aligners? by swbarnes2 11k
I think for time's sake a not-splice aware aligner isn't going to search horribly far away for the other half of a read, while a splice-awa…
Comment: Beginner problem: installed python3.7.12 but py_available() return FALSE by Sashu • 0
Anyway, thanks your reply!
Comment: Automatic Outlier Detection for RNA-seq data by simplitia ▴ 60
@kevin thank is a great answer. We are having the same issue with outliers. With the 2nd part using > 3 SD; do you have a reference for …
Comment: How to use MACS2 output for DESEQ2 differential analysis during ATAC-seq? How to by Papyrus ★ 1.3k
Take a look at the [DiffBind][1] R package (which internally uses `DESeq2`, or `edgeR`), the tutorial [vignette][2] is quite extensive. …
Comment: Beginner problem: installed python3.7.12 but py_available() return FALSE by Sashu • 0
I forget to tell that I have followed the error message but this problem still existed...
Comment: Beginner problem: installed python3.7.12 but py_available() return FALSE by jared.andrews07 ★ 11k
Follow the error message. Allow reticulate to handle the python environment itself.
Comment: How to perform DE anaysis on a data set in which biological replicates have high by Gisele • 0
Thank you! This is my next step to try to understand what is the best choice.
Comment: Error message running GeMoMa by Dardo • 0
can you solve this problem? this is my problem too
Comment: How to download BLAST+ on Centos (6) by Nelo • 0
okie Tnkq
Comment: Need help to remove NA values from data frame by ponganta ▴ 490
Agreed, especially regarding `dplyr::rename()`. I didn't think about that. Regarding these two functions, there are oftentimes namespace …
Comment: blast culling_limit option behavior by joe.westley • 0
Hi GenoMax, sorry for the late response. Yes I am looking to only keep one hit. I am not sure I follow the idea that all the reported hit…
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