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738 results • Page
1 of 15
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Votes
Replies
76
votes
72
replies
20k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
23 days ago by
Kevin Blighe
88k
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 29 days ago by
kjngo
• 0 • written 12.1 years ago by
Gabriel R.
★ 2.9k
40
votes
10
replies
43k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 18 days ago by
cwwong13
▴ 40 • written 6.8 years ago by
lessismore
★ 1.3k
38
votes
24
replies
2.3k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 18 days ago by
i.sudbery
19k • written 20 days ago by
noodle
▴ 580
38
votes
12
replies
31k
views
9 follow
How to systematically check if a bam file is truncated
Exomeseq
updated 22 hours ago by
alanh
▴ 170 • written 7.1 years ago by
jonessara770
▴ 240
34
votes
16
replies
21k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read
length
bam
updated 29 days ago by
Hagen
▴ 10 • written 10.3 years ago by
filipzembol
▴ 180
29
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split
fastq
updated 15 days ago by
thomas.heigl.ibk
• 0 • written 12.8 years ago by
Bioscientist
★ 1.7k
25
votes
11
replies
3.8k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 24 days ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
22
votes
18
replies
6.2k
views
about batch correction in scRNA-seq
scRNA
scRNA-seq
batch-effect
updated 29 days ago by
Ram
43k • written 4.6 years ago by
Bogdan
★ 1.4k
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 22 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
16
votes
12
replies
7.5k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome
perl
python3
bash
python
updated 15 days ago by
rsieber
▴ 10 • written 3.2 years ago by
Kumar
▴ 120
14
votes
2
replies
7.1k
views
Trouble with Pilon installation
polishing
pilon
installation
updated 23 days ago by
Lissa Cruz Saavedra
• 0 • written 7.3 years ago by
Rox
★ 1.4k
13
votes
14
replies
948
views
High Malat-1 expression in single cell data
single-cell
updated 10 days ago by
t.montserrat.ayuso
▴ 40 • written 19 days ago by
carolofharvest
▴ 40
11
votes
3
replies
345
views
TFs and Gene databases
Transcription-factor
Target
Regulatory-Networks
updated 10 days ago by
b.contreras.moreira
▴ 200 • written 10 days ago by
ijarne
• 0
11
votes
12
replies
1.2k
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 29 days ago by
Ram
43k • written 29 days ago by
iamsmor
• 0
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 11 days ago by
Pierre Lindenbaum
161k • written 5.8 years ago by
mostafarafiepour
▴ 180
10
votes
6
replies
10k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly
rna-seq
alignment
updated 22 days ago by
Antonio R. Franco
★ 5.1k • written 6.0 years ago by
williamsbrian5064
▴ 520
10
votes
14
replies
790
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 11 days ago by
GenoMax
142k • written 16 days ago by
nicole.kavanagh
• 0
9
votes
10
replies
7.0k
views
Harmony batch correction vs. regressing out donor effect in Seurat
Seurat
scRNA-seq
Harmony
RNA-seq
batch-effect
updated 29 days ago by
Ram
43k • written 4.6 years ago by
Lucy
▴ 140
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 7 days ago by
Ruqaiya
• 0 • written 5.7 years ago by
xiaozhongzhiping
▴ 20
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation
reference panel
updated 7 days ago by
analyst
▴ 50 • written 6.4 years ago by
David_emir
▴ 490
9
votes
23
replies
9.8k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
7 days ago by
vytarasov
▴ 180
9
votes
3
replies
7.0k
views
EdgeR-GLMs correcting for batch effects
RNA-Seq
edgeR
Batch-Effect
updated 29 days ago by
Ram
43k • written 10.0 years ago by
Matina
▴ 250
8
votes
5
replies
6.5k
views
ISCN annotation for SV/CN VCF files
SV
written 8 months ago by
a.beggs
▴ 60
8
votes
8
replies
764
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 23 days ago by
swbarnes2
14k • written 24 days ago by
Aaliya
▴ 10
8
votes
16
replies
1.2k
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 21 days ago by
bk11
★ 2.5k • written 10 weeks ago by
Sofia
• 0
7
votes
1
reply
197
views
Tutorial:
removeBatchEffect explained using base R linear models
limma
effects
batch
removebatcheffects
updated 11 days ago by
dariober
14k • written 11 days ago by
nhaus
▴ 360
7
votes
3
replies
3.0k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 29 days ago by
colindaven
6.4k • written 16 months ago by
Dr.Animo
▴ 130
7
votes
16
replies
955
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
19 days ago by
Ruqaiya
• 0
7
votes
6
replies
600
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
26 days ago by
analyst
▴ 50
7
votes
2
replies
330
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 24 days ago by
geneontologyhelp
▴ 400 • written 25 days ago by
catherine.teyssier
• 0
7
votes
7
replies
6.0k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 22 days ago by
rohitsatyam102
▴ 860 • written 6.2 years ago by
smallfish
▴ 10
6
votes
7
replies
393
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
5 days ago by
sansan_96
▴ 90
6
votes
4
replies
297
views
Details on salmon index
Salmon
updated 1 day ago by
Rob
6.6k • written 2 days ago by
Lorenzo
• 0
6
votes
0
replies
2.6k
views
Tool:
Immuno-Navigator, a batch-corrected database for gene coexpression in the immune system
gene-co-expression
batch-effect
immunology
updated 29 days ago by
Ram
43k • written 7.1 years ago by
alexis.vandenbon
▴ 80
6
votes
3
replies
230
views
Interpretting IGV output
IGV
updated 26 days ago by
Carlo Yague
8.7k • written 26 days ago by
analyst
▴ 50
6
votes
2
replies
243
views
EdgeR - relationship between logFC and coefficients
differential-expression
r
edger
updated 8 days ago by
Gordon Smyth
★ 7.2k • written 8 days ago by
gBioStar5
▴ 10
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat
RNA-Seq
Limma
DESeq2
batch-effect
updated 29 days ago by
Ram
43k • written 5.0 years ago by
borkk
▴ 140
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 6 days ago by
Ruqaiya
• 0 • written 6.7 years ago by
maple964
• 0
6
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon
human
bed
v7
agilent
all
sureselect
updated 12 days ago by
MiladAD
▴ 10 • written 2.0 years ago by
soheil
• 0
6
votes
4
replies
440
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
16 days ago by
Estevão
▴ 10
6
votes
4
replies
13k
views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic
paired-end
updated 7 days ago by
Ruqaiya
• 0 • written 6.5 years ago by
dllopezr
▴ 130
6
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing
coverage
3 days ago by
Arton
▴ 10
5
votes
5
replies
321
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
10 days ago by
Chris
▴ 280
5
votes
5
replies
347
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 16 days ago by
atharvakarkare14
▴ 40 • written 16 days ago by
Begonia_pavonina
▴ 150
5
votes
2
replies
439
views
Missing protein (VEGF-A) in String db
VGFA
stringdb
updated 22 days ago by
shalespringer
▴ 10 • written 3 months ago by
Phenylananin
▴ 20
5
votes
2
replies
350
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 19 days ago by
i.sudbery
19k • written 21 days ago by
vanbelj
▴ 40
5
votes
13
replies
2.0k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 28 days ago by
ATpoint
82k • written 29 days ago by
BioinfGuru
★ 1.7k
5
votes
6
replies
605
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 17 days ago by
me
▴ 760 • written 19 days ago by
Mariana
▴ 40
5
votes
5
replies
671
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 14 days ago by
Mbofire
• 0 • written 23 days ago by
Ming Tommy Tang
★ 3.9k
738 results • Page
1 of 15
Recent Votes
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
Answer: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
C: How can I perform Differential expression analysis with just one control and one
C: How can I perform Differential expression analysis with just one control and one
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Comment: calculating genomic coverage/ base overlap in R
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1769mkc
★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
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82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
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21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
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★ 7.2k
See the exploration of isoform precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Table 1 o…
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txema.heredia
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Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
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▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
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hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
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Yes, `bedmap` will perform operations on one or two BED files.
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Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
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14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
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4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot
by
bk11
★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool
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ntsopoul
▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
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