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13,538 results • Page
3 of 271
Sort: replies
Rank
Views
Votes
Replies
36
votes
25
replies
32k
views
15 follow
Downsampling dataset with more than 60 million reads
next-gen
RNA-Seq
updated 4 months ago by
asalimih
▴ 60 • written 9.7 years ago by
mike
▴ 90
6
votes
25
replies
38k
views
14 follow
CluserProfiler message "No gene can be mapped"
R
updated 11 months ago by
13554221497
• 0 • written 6.1 years ago by
ARich
▴ 130
38
votes
25
replies
9.1k
views
13 follow
FASTA file of fixed length
sequence
fasta
updated 7 months ago by
Ram
43k • written 8.1 years ago by
waqasnayab
▴ 250
18
votes
25
replies
15k
views
13 follow
Easy way to split VCF file by chromosome
sequence
TOPMED
chromosome
Imputation
SNP
updated 10 months ago by
Pierre Lindenbaum
161k • written 2.3 years ago by
ConvolutedGenome
▴ 30
17
votes
25
replies
2.4k
views
Tool:
Platform for Bioinformatics Students, Scholars and Scientists
sequence
genome
updated 10 months ago by
Ram
43k • written 8.2 years ago by
support
▴ 50
51
votes
25
replies
6.9k
views
10 follow
What Is Your Experience With Bioinformatics Webservices?
web-service
subjective
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Michael
54k
60
votes
25
replies
22k
views
17 follow
Which Operating System Do You Prefer For Bioinformatics?
general
subjective
updated 6 months ago by
Ram
43k • written 14.3 years ago by
Giovanni M Dall'Olio
28k
13
votes
25
replies
11k
views
9 follow
Tool:
Mitcr: A Software Tool For Analyzing T-Cell Receptor Sequencing Data
analysis
sequencing
ngs
updated 10 months ago by
Ram
43k • written 10.7 years ago by
mikhail.shugay
3.5k
60
votes
25
replies
5.5k
views
8 follow
Forum:
Am I crazy, or are most published RNA-seq studies vastly underpowered?
sample-size
statistical-power
RNA-Seq
updated 10 months ago by
Ram
43k • written 3.7 years ago by
telroyjatter
▴ 230
13
votes
25
replies
4.3k
views
7 follow
VEP output has no gene names
alignment
sequencing
vep
updated 11 months ago by
barslmn
★ 2.1k • written 5.7 years ago by
Gene_MMP8
▴ 240
64
votes
24
replies
3.0k
views
12 follow
Forum:
How much I must feel useless?
machine-learning
Programming
statistics
updated 11 months ago by
Ram
43k • written 5.6 years ago by
Molecular_genetics
▴ 80
87
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 11 days ago by
Gordon
• 0 • written 3.5 years ago by
Hamid Ghaedi
3.2k
159
votes
24
replies
62k
views
19 follow
Recommended Tools For Alternative Splicing Detection From Rna-Seq Data
alternative-splicing
splicing
rna-seq
updated 10 months ago by
Ram
43k • written 11.2 years ago by
Nicolas Rosewick
11k
15
votes
24
replies
2.6k
views
7 follow
Forum:
Airport.bio: First class ticket to any biological database in the world
RNA-Seq
ChIP-Seq
SNP
updated 11 months ago by
Ram
43k • written 6.1 years ago by
Bohdan Khomtchouk
▴ 350
20
votes
24
replies
6.9k
views
6 follow
Forum:
Python or R
RNA-Seq
alignment
next-gen-sequencing
updated 11 months ago by
Ram
43k • written 5.9 years ago by
Qingyang Xiao
▴ 160
80
votes
24
replies
11k
views
18 follow
Which Bioinformatics Journals Do You Follow?
bioinformatics-journal
updated 5 months ago by
Ram
43k • written 14.0 years ago by
Giovanni M Dall'Olio
28k
65
votes
24
replies
17k
views
14 follow
Mapping Snps To Pathways
snp
genotyping
pathway
gene
enrichment
updated 6 months ago by
Ram
43k • written 14.2 years ago by
Pierre Lindenbaum
161k
27
votes
24
replies
2.4k
views
7 follow
Code Golf - bisulfite conversion
bisulfite
bsseq
code-golf
updated 11 months ago by
Ram
43k • written 5.6 years ago by
Chris Miller
22k
48
votes
24
replies
8.2k
views
14 follow
Tool:
Hera: A new tool for RNA-Seq analysis
kallisto
RNA-Seq
STAR
gene-fusion
updated 10 months ago by
Ram
43k • written 6.8 years ago by
sonpham
▴ 580
4
votes
24
replies
6.0k
views
Split a concatenated alignment in multiple files
alignment
fasta
updated 6 months ago by
Felipe
• 0 • written 9.1 years ago by
dago
★ 2.8k
66
votes
23
replies
49k
views
8 follow
extract dendrogram cluster from pheatmap
R
updated 6 weeks ago by
Getnet Tesfaw
• 0 • written 6.4 years ago by
1769mkc
★ 1.2k
33
votes
23
replies
4.2k
views
8 follow
Forum:
Is there a file format better suited for the era of pangenomics than the .vcf? What are its attributes?
VCF
file-format
genomics
updated 10 months ago by
Jeremy Leipzig
22k • written 10 months ago by
LauferVA
4.2k
34
votes
23
replies
21k
views
12 follow
Is there a tool that sorts gtf files?
RNA-Seq
genome
updated 7 months ago by
alejandrogzi
▴ 120 • written 6.1 years ago by
JJ
▴ 680
6
votes
23
replies
1.4k
views
How to speed Salmon index up
metagenome
genome
salmon
3 months ago by
young_bioinformatician
▴ 230
40
votes
23
replies
4.2k
views
12 follow
Forum:
Why learn programming in bioinformatics?
Programming
updated 11 months ago by
Ram
43k • written 5.7 years ago by
joselu
▴ 110
12
votes
23
replies
8.3k
views
6 follow
motif search with ATAC-seq
motif-search
ATAC-seq
updated 10 months ago by
Ram
43k • written 5.6 years ago by
grant.hovhannisyan
★ 2.6k
23
votes
23
replies
9.9k
views
6 follow
How to see if adjusting batch effect in RNA-seq is working or not
RNA-Seq
removeBatchEffect
batch-effect
edger
updated 12 days ago by
Ram
43k • written 5.3 years ago by
iraia.munoa
▴ 130
31
votes
23
replies
30k
views
15 follow
Amino Acid Change To Genomic Location
snp
amino-acids
updated 3 months ago by
gernophil
▴ 80 • written 12.3 years ago by
Preethi
▴ 110
93
votes
23
replies
92k
views
15 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 3 months ago by
clara.apicella
• 0 • written 5.8 years ago by
otwtgin2010
▴ 610
18
votes
23
replies
7.7k
views
7 follow
How to exclude some of breast cancer subtypes just by looking at gene expression?
RNA-Seq
genome
cancer
gene
updated 10 months ago by
Safu
• 0 • written 6.4 years ago by
jack
▴ 960
56
votes
23
replies
5.0k
views
10 follow
Tool:
ASCIIGenome: Text Only Genome Viewer!
terminal
genome-browser
java
ASCIIGenome
updated 10 months ago by
Ram
43k • written 7.8 years ago by
dariober
14k
6
votes
23
replies
26k
views
6 follow
devtools Installation error in R (version 3.5.3)?
github
R
phylogeny
devtools
updated 11 months ago by
Ram
43k • written 5.1 years ago by
Kumar
▴ 120
20
votes
23
replies
7.2k
views
6 follow
Tool:
EaSeq - Interactive ChIP-seq analysis and visualization (for Windows)
easeq
Windows
Visualization
ChIP-Seq
updated 10 months ago by
Ram
43k • written 8.1 years ago by
Mads Lerdrup
▴ 460
61
votes
23
replies
57k
views
15 follow
How Can I Know The Length Of Mapped Reads From Bam File?
bam
mapping
updated 5 months ago by
Lluís R.
★ 1.2k • written 11.2 years ago by
Jordan
★ 1.3k
39
votes
23
replies
34k
views
11 follow
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools
updated 8 months ago by
s.w.vanderlaan
▴ 40 • written 2.8 years ago by
Michal Nevo
▴ 130
66
votes
23
replies
11k
views
9 follow
Using Hdf5 To Store Bio-Data
hdf5
storage
database
updated 6 months ago by
Ram
43k • written 14.2 years ago by
Pierre Lindenbaum
161k
11
votes
23
replies
1.7k
views
gatk Hardfilter Error
hardfilter
updated 11 months ago by
Michael
54k • written 11 months ago by
bestone
▴ 30
11
votes
22
replies
4.2k
views
No significant DEG: A request to double check my commands for limma.
limma
differential-gene-expression
updated 20 days ago by
Ram
43k • written 5.0 years ago by
RNAseqer
▴ 260
3
votes
22
replies
4.0k
views
GRanges objects don't support [[, as.list(), lapply(), or unlist() at the moment
GRanges
updated 10 months ago by
Amitm
★ 2.2k • written 14 months ago by
Antonia
• 0
1
vote
22
replies
2.1k
views
error with Tximport when txOut = TRUE
tximport
R
updated 9 months ago by
Ram
43k • written 9 months ago by
mbansal
• 0
28
votes
22
replies
57k
views
11 follow
How To Convert List Of Entrez Ids Into Gene Name
r
genomics
entrez
updated 10 months ago by
cwang3444
• 0 • written 11.0 years ago by
grosy
▴ 90
31
votes
22
replies
13k
views
6 follow
Tool:
SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
FASTQ
SeqKit
FASTA
updated 10 months ago by
Ram
43k • written 7.6 years ago by
shenwei356
8.4k
9
votes
22
replies
9.7k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
9 months ago by
vytarasov
▴ 180
26
votes
22
replies
13k
views
10 follow
Tool:
BBSketch - A Tool for Rapid Sequence Comparison
minhash
sketch
bbmap
blast
updated 11 months ago by
Ram
43k • written 7.2 years ago by
Brian Bushnell
20k
34
votes
22
replies
2.9k
views
11 follow
Forum:
Have we failed as bioinformatician in this time of COVID-19
Bioinformatician
COVID-19
updated 10 months ago by
Ram
43k • written 4.0 years ago by
heididunst
▴ 10
12
votes
22
replies
1.8k
views
Can anyone simplify GATK installation
GATK
3 months ago by
Tundup
• 0
34
votes
22
replies
1.5k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
4 hours ago by
noodle
▴ 570
57
votes
22
replies
29k
views
7 follow
Batch correction in DESeq2
Combat
DESeq2
Batch-Effect
updated 24 days ago by
Ram
43k • written 4.5 years ago by
Arindam Ghosh
▴ 510
24
votes
22
replies
27k
views
11 follow
replace fasta headers with another name in a text file
perl
updated 10 months ago by
nr299
• 0 • written 9.9 years ago by
Jemo
▴ 60
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch-effect
updated 12 days ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
13,538 results • Page
3 of 271
Recent Votes
Comment: High Malat-1 expression in single cell data
Answer: Extract protein sequence
Answer: Extract protein sequence
C: How do I ask a question on Biostars?
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
Comment: How to calculate identity percentage between proteins contained in a FASTA file?
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Recent Replies
Comment: Perfom a Gene Ontology Analysis from GO terms txt file
by
sansan_96
▴ 80
Your table should look like this (GO terms): ``` geneid GOid Zm00001eb000010 GO:0003690;GO:0003727;GO:0019843;GO:0005739 Zm00001eb000020 G…
Answer: Perfom a Gene Ontology Analysis from GO terms txt file
by
sansan_96
▴ 80
I understand, here is an example with topGO where you need a differential expression table (DESeq2 for example) and a table of GO terms: `…
Comment: Perfom a Gene Ontology Analysis from GO terms file
by
Hamtaro
▴ 50
Thank u for your reply. The problem is that I used the genome and gene annotation from that webpage, not ensemble or ncbi, so I have to use…
Comment: Perfom a Gene Ontology Analysis from GO terms file
by
sansan_96
▴ 80
Hello, To perform functional enrichment analysis there are packages such as topGO or clusterProfiler that can work very well. Lately I've …
Answer: Post-imputation plot
by
LChart
3.9k
The anti-diagonal band does suggest some fraction of genotypes are strand-flipped - probably G/C or A/T variants.
Comment: Differential Accessibility
by
Ram
43k
Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the cod…
Comment: Extract protein sequence
by
anna
▴ 20
Thank you! I need this for eukaryotic organism and known protein sequences, but I guess seqkit would work well!
Comment: Landmark gene selection in L1000.
by
GenoMax
141k
Paper referred to in question: https://pubmed.ncbi.nlm.nih.gov/29195078/ > so I want to understand how you reduced the 12063 genes to 978…
Comment: What should I consider as FASTA for dataset?
by
Nafi
• 0
Protein attribute prediction
Comment: Batch effects : ComBat or removebatcheffects (limma package) ?
by
cwwong13
▴ 40
@kevin May I know whether your comments and edits were mainly based on the fact that "Previously, [crazy] people had been using the origina…
Comment: Programmatically retrieving positions of protein active site residues
by
Wayne
★ 2.0k
Wow, I was shocked at this AI answer that looks to be a good start for using UniProt. Sharing it in case it is useful. (It will work in ses…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 570
> Can you clarify what you mean by "100% of reads pass cutadapt, even > though 70% of reads contain adapters and get trimmed. The header o…
Comment: Software to separate reads from different individuals
by
GenoMax
141k
If you have independent information available (e.g. genotype data for both individuals) then you *may* be able to assign reads based on the…
Answer: Extract protein sequence
by
Matthias Zepper
4.5k
You didn't mention what kind of organism you are working with and what kind of protein you are looking for? If it happens to be a microbia…
Comment: How to use limma to find differentially expressed genes in response to a continu
by
pairedttest
▴ 10
Thank you Gordon for your expertise. One question that I have now that I have a list of DE genes is how to interpret logFC of this continuo…
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