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1,000 results • Page
6 of 20
Sort: Views
Rank
Views
Votes
Replies
63
votes
16
replies
43k
views
11 follow
How To Analyze Imputed Gwas Data
gwas
r
snp
imputation
plink
updated 3.9 years ago by
Mahan
▴ 70 • written 13.2 years ago by
Stephen
2.8k
25
votes
6
replies
43k
views
Aggregate multiple rows based on common values in given columns
R
updated 5.6 years ago by
zx8754
11k • written 8.5 years ago by
writersblog02
▴ 70
48
votes
33
replies
43k
views
16 follow
Extract A Group Of Fasta Sequences From A File
fasta
python
perl
biopython
bioperl
updated 2.4 years ago by
Ram
43k • written 13.8 years ago by
Kyle
▴ 60
2
votes
4
replies
43k
views
python 3.8 'No module named pip'
rna-seq
updated 2.9 years ago by
linehammer
▴ 10 • written 3.8 years ago by
amandanm
• 0
105
votes
26
replies
43k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation
domain
r
updated 7 months ago by
zx8754
11k • written 11.3 years ago by
henryvuong
▴ 810
15
votes
12
replies
43k
views
8 follow
Intall local BLAST in Ubuntu
blast
local
system
requirement
Ubuntu
updated 3.9 years ago by
brian.fristensky
▴ 460 • written 6.7 years ago by
Kanchana Sankalpa
▴ 30
20
votes
4
replies
43k
views
what does a log 2-fold change values of mean ?
motif
microarray
gene
genesequencing
sequencing
5.5 years ago by
a4appy23
▴ 50
81
votes
21
replies
43k
views
15 follow
How To Get Bed File Containing Exons Of Canonical Transcripts And Their Corresponding Gene Symbols
bed
transcript
ucsc
biomart
updated 7 months ago by
Joel Wallenius
▴ 210 • written 10.2 years ago by
pristanna
▴ 750
39
votes
17
replies
43k
views
13 follow
Extract Cds Fastas From A Gff Annotation + Reference Sequence
gff
CDS
updated 15 months ago by
Ram
43k • written 11.9 years ago by
Federico Giorgi
▴ 730
40
votes
4
replies
43k
views
What Is Snp Calling?
snp
next-gen
sequencing
snp
updated 13.3 years ago by
Joesoap
• 0 • written 14.0 years ago by
Giovanni M Dall'Olio
28k
10
votes
16
replies
43k
views
6 follow
Beginner in Python- need in assistance translating DNA into protein sequence
python
updated 3.3 years ago by
maram.mostafa08800
• 0 • written 7.4 years ago by
oki4
▴ 10
18
votes
6
replies
42k
views
How can I convert -log10 (p-value) to p-value?
p-value
updated 18 months ago by
1769mkc
★ 1.2k • written 5.3 years ago by
somayeh bakhshalizadeh
▴ 80
45
votes
7
replies
42k
views
9 follow
Any Good Bam And Sam Viewer?
viewer
sam
bam
updated 2.3 years ago by
Ram
43k • written 12.6 years ago by
Ken
▴ 160
60
votes
12
replies
42k
views
10 follow
Get chromosome sizes from fasta file
genome
ucsc
updated 18 months ago by
jamesogilvie1
• 0 • written 8.3 years ago by
rioualen
▴ 710
40
votes
13
replies
42k
views
8 follow
Difference between FC and LogFC
r
microarray
updated 2.3 years ago by
琪
• 0 • written 6.0 years ago by
Joe Kherery
▴ 120
40
votes
10
replies
42k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 7 days ago by
cwwong13
▴ 40 • written 6.8 years ago by
lessismore
★ 1.3k
26
votes
13
replies
42k
views
7 follow
what is the difference between GRCh37 and hg19 ?
RNA-Seq
Assembly
genome
alignment
updated 2.2 years ago by
Ram
43k • written 9.4 years ago by
jack
▴ 960
23
votes
4
replies
42k
views
What is the difference between GTF AND GFF format
RNA-Seq
updated 10.0 years ago by
jason
▴ 160 • written 10.0 years ago by
Y Tb
▴ 230
14
votes
6
replies
42k
views
7 follow
How To Convert A Fasta Or Alignment File To Nexus (.Nex) File That Is To Be Used In The Beast Program
updated 20 months ago by
kamiljaron
▴ 220 • written 10.7 years ago by
triinlakspere
▴ 20
42
votes
21
replies
42k
views
11 follow
Comparing 2 Large Lists (Millions Of Rows) To Identify Shared And Exclusive Elements
unix
list
intersect
updated 2.5 years ago by
Ram
43k • written 11.3 years ago by
Bioinfosm
▴ 620
46
votes
9
replies
42k
views
9 follow
How To Convert Centimorgan To Base Pair
genetics
distance
updated 19 months ago by
Ram
43k • written 12.3 years ago by
Aurgha
▴ 90
16
votes
5
replies
42k
views
Understand Samtools View Output
samtools
updated 2.5 years ago by
Ram
43k • written 12.9 years ago by
Zhshqzyc
▴ 520
64
votes
24
replies
42k
views
12 follow
How to extract unique mapped results from Bowtie2 bam results?
alignment
updated 16 months ago by
Ram
43k • written 10.0 years ago by
zhwjmch
▴ 170
33
votes
4
replies
42k
views
What read lengths are produced by modern Illumina sequencers?
read-length
dna
illumina
updated 2.3 years ago by
Ram
43k • written 9.9 years ago by
John Smith
▴ 320
4
votes
4
replies
42k
views
How to convert a URL into a DOI programmatically
pubmed
doi
url
written 7.6 years ago by
entheologist33
▴ 100
53
votes
21
replies
41k
views
12 follow
How To Filter Multi Fasta By Length??
awk
updated 5.8 years ago by
Ram
43k • written 10.7 years ago by
HG
★ 1.2k
29
votes
5
replies
41k
views
What Does Up-Regulated And Down-Regulated Mean?
updated 2.4 years ago by
BioNerd
• 0 • written 12.0 years ago by
kate
▴ 100
18
votes
5
replies
41k
views
R - pheatmap - changing column order
pheatmap
heatmap
R
updated 2.4 years ago by
Ram
43k • written 9.8 years ago by
piotr.grabowski
▴ 60
13
votes
8
replies
41k
views
6 follow
Bowtie2 Ubuntu Installation
ubuntu
bowtie
updated 3.3 years ago by
saritamaurya
• 0 • written 11.7 years ago by
Nasrin
▴ 30
50
votes
21
replies
41k
views
11 follow
How Do You Justify Your Rna-Seq Expression Threshold (Fpkm/Rpkm) ?
rpkm
rna-seq
cutoff
fpkm
updated 2.5 years ago by
Ram
43k • written 11.3 years ago by
biorepine
★ 1.5k
26
votes
19
replies
41k
views
7 follow
Fasta File Vs Fa File
fasta
sequence
updated 12.9 years ago by
brentp
24k • written 12.9 years ago by
Zhshqzyc
▴ 520
33
votes
12
replies
41k
views
8 follow
How To Find Paralogs Using Blast
homology
blast
updated 12.1 years ago by
Larry_Parnell
16k • written 12.8 years ago by
ngsgene
▴ 380
206
votes
58
replies
41k
views
31 follow
Forum:
Will Python Take The Place Of R?
r
statistics
python
biopython
updated 14 months ago by
Ram
43k • written 11.0 years ago by
Medhat
9.7k
49
votes
23
replies
41k
views
13 follow
Concatenating fastq.gz files across lanes
RNA-Seq
updated 2.2 years ago by
D
▴ 10 • written 5.9 years ago by
volvicpellegrino
▴ 40
42
votes
4
replies
41k
views
What Control For Chip-Seq: Input, Igg Or Untagged Strain?
chip-seq
updated 12.4 years ago by
Ying W
★ 4.2k • written 12.4 years ago by
Olbzn
▴ 180
6
votes
7
replies
41k
views
6 follow
Bowtie Building Index Issue
bowtie
bowtie2
genome
updated 11.9 years ago by
Istvan Albert
100k • written 11.9 years ago by
Arpssss
▴ 40
82
votes
13
replies
41k
views
7 follow
Ti/Tv Ratio Confirms Snp Discovery. Is This A General Rule?
snp
snp
updated 3.7 years ago by
Biostar
20 • written 13.3 years ago by
Yahan
▴ 210
27
votes
12
replies
41k
views
7 follow
Log2 Ratio or Log2 Fold Change - terminology confusion and which one should I use?
genome
updated 21 months ago by
obidobi
▴ 30 • written 7.5 years ago by
Genosa
▴ 160
17
votes
7
replies
41k
views
6 follow
Calculating Genomic Inflation Factor
gwas
plink
updated 7.3 years ago by
GabrielMontenegro
▴ 670 • written 12.0 years ago by
Debs
▴ 30
52
votes
14
replies
40k
views
15 follow
Converting Bam To Fastq
next-gen-sequencing
fastq
updated 5 months ago by
Pierre Lindenbaum
161k • written 14.1 years ago by
Zach Stednick
▴ 660
6
votes
11
replies
40k
views
Finding The Mean Of Values In A Single Column
r
updated 10.5 years ago by
Michael
54k • written 10.5 years ago by
robjohn7000
▴ 110
13
votes
10
replies
40k
views
7 follow
How To Uncompress The 1000 Genome Vcf.Gz File
updated 2.7 years ago by
tcarter.era
• 0 • written 11.5 years ago by
GPR
▴ 390
17
votes
25
replies
40k
views
7 follow
Remove columns and rows which have only NAs without deleting all the data
missing data
R
correlation
SNPs
updated 5.4 years ago by
slegotsky
• 0 • written 6.8 years ago by
ElenaL
• 0
28
votes
10
replies
40k
views
6 follow
Extract subset of samples from multigenome vcf file
vcf
8.1 years ago by
MAPK
★ 2.1k
35
votes
11
replies
40k
views
9 follow
Is It Possible To Get Fragment Length, Read Length And Number Of Fragments From A Bam/Sam File
bam
next-gen
updated 7.4 years ago by
jerry
▴ 130 • written 11.2 years ago by
samsara
▴ 630
58
votes
25
replies
40k
views
15 follow
Tutorial:
Protocol To Downlad TCGA Data From GDC
GDC
methylation
TCGA
updated 13 months ago by
Ram
43k • written 7.8 years ago by
Shicheng Guo
★ 9.4k
36
votes
8
replies
40k
views
9 follow
Difference Between "Mate Pair" And "Pair-End"
paired-end
ngs
library
updated 17 months ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
weiqiangduan
▴ 150
160
votes
19
replies
40k
views
16 follow
Why Does Rna-Seq Read Count Fit Poisson Distribution?
rna-seq
modeling
updated 2.4 years ago by
Ram
43k • written 10.5 years ago by
sckinta
▴ 730
15
votes
2
replies
40k
views
what is difference between sequence adapter and PCR primer?
adapter
pcr
updated 16 months ago by
Ram
43k • written 8.9 years ago by
xiangwulu
▴ 120
16
votes
8
replies
40k
views
7 follow
LogFC and LogCPM
rna-seq
updated 2.9 years ago by
mohammedtoufiq91
▴ 250 • written 7.0 years ago by
silas008
▴ 170
1,000 results • Page
6 of 20
Recent Votes
Comment: Which hg38 file?
Answer: Which hg38 file?
Answer: Where to get the following bed file?
How to save GRanges object to csv file
Answer: How to get proteins from GFF file resulted from MAKER annotation
Answer: Gene ontology and homologs
Comment: anRichment is missing
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Comment: Where to get the following bed file?
by
GenoMax
142k
SeqCap kits are discontinued. If you don't find the said file your will need to email Roche Support per this page: https://sequencing.roche…
Answer: Where to get the following bed file?
by
LChart
3.9k
UCSC maintains a list of exome probe sets and targets. You could check there: https://hgdownload.soe.ucsc.edu/gbdb/hg19/exomeProbesets/
Comment: How to compute TPM normalized values for TCGA miRNA data?
by
Ngrin
• 0
Yes, I found some similar ideas on biostar repository. So you think the authors have done something wrong? And I should only consider CPM?
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
▴ 390
It is difficult to answer how they were able to identify *S. hominis* without seeing the code or paper. To address your second question, i…
Comment: Problem with Seurat package in PercentageFeatureSet function
by
bk11
★ 2.4k
Did you check where the `features.tsv.gz` file had Gene IDs or Ensembl IDs?
Answer: How to compute TPM normalized values for TCGA miRNA data?
by
dsull
★ 6.0k
TPM is irrelevant for miRNA-seq; CPM works fine. TPM tries to adjust for length effects by dividing by gene length (e.g. reducing the im…
Comment: Applying the metacell2 algorithm using python
by
Wayne
★ 2.0k
"I'm also unsure what qualifies as a lateral gene." The [README where you reference](https://metacells.readthedocs.io/en/latest/readme.htm…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
sovrappensiero
▴ 90
Ah, yes this makes sense! I knew this was an issue with, say, using kraken2 on shotgun metagenomic reads, but I don't have a lot of experi…
Comment: How to access TCGA samples that were treated with a specific drug?
by
Qroid
▴ 40
Thank you. Maybe it's best to confirm with the authors about how they're getting responder/non-responder labels. I'll do that now.
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
▴ 390
If you sequenced a short hypervariable region, most of your sequence reads will not be able to be assigned to the species level. One possi…
Comment: anRichment is missing
by
GenoMax
142k
Consider emailing Dr. Horvath about this. Until enough people make him aware of this issue WGCNA "problem" is unlikely to get fixed.
Comment: anRichment is missing
by
Tatyana
• 0
Unfortunately, there are only tutorials and codes for tutorials for WGCNA, not installation files for any their packages... :(
Comment: anRichment is missing
by
GenoMax
142k
See this link for the WGCNA documentation and code from Peter Langfelder : https://bioinformatics.stackexchange.com/questions/21885/where-t…
Comment: anRichment is missing
by
Tatyana
• 0
The problem is back, Horwath's lab web is down again. Is it possible to get anRichment istallation file somewhere? (The greater problem is …
Comment: 16S rRNA microbiome differential abundance analysis with DESeq2 finds same micro
by
andres.firrincieli
3.6k
1. Maribaculaceae is a family not a genus 2. Who said that ASV with the same taxonomic classification must have the same behaviour? 3. With…
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