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112,641 results • Page
1 of 2253
Sort: Rank
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Votes
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0
votes
0
replies
3
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Comparison of BED files
BED
NGS
Comparison
10 minutes ago by
adarsh_pp
▴ 30
0
votes
4
replies
611
views
Can vg take MUMmer output as input?
vg
updated 32 minutes ago by
Qi
• 0 • written 2.8 years ago by
ac2278
▴ 20
0
votes
0
replies
11
views
Bacterial Pangenome Analysis
Pathogenic
Prokka
Roary
Pangenome
bacteria
1 hour ago by
kirankumareripogu
▴ 10
2
votes
4
replies
1.8k
views
Samtools Failing to Install through Conda
samtools
conda
updated 4 hours ago by
hukai916
▴ 10 • written 17 months ago by
jjp55
▴ 20
0
votes
0
replies
50
views
Violin plot (Monocle 3) - Troubleshooting
Monocle3
updated 6 hours ago by
GenoMax
134k • written 6 hours ago by
sharic0010
• 0
3
votes
7
replies
238
views
Should I Learn Docker to Run Command Line Bioinformatics Tool?
Docker
updated 7 hours ago by
Yogi
▴ 10 • written 14 hours ago by
arriyaz.nstu
▴ 30
0
votes
1
reply
71
views
GO analysis after DESeq2
GO
updated 7 hours ago by
Ram
40k • written 7 hours ago by
oduduabasi.isaiah
• 0
762
votes
162
replies
123k
views
105 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 6 weeks ago by
Biostar
2.0k • written 6.8 years ago by
Istvan Albert
98k
0
votes
1
reply
77
views
Program for Overlapping DMRs (Differentially Methylated Regions) Between Groups
methylation
DMR
updated 8 hours ago by
LChart
3.3k • written 8 hours ago by
epianalysis
• 0
0
votes
1
reply
94
views
Saving the output of LD pruning from SNPRelate package as a new GDS file
LD-pruning
SNPRelate
updated 8 hours ago by
Ram
40k • written 11 hours ago by
Patrick
• 0
0
votes
0
replies
56
views
News:
New NCBI Datasets APIs to Replace Old Ones
NCBI
API
Datasets
9 hours ago by
PeterC_NCBI
▴ 330
1
vote
3
replies
162
views
miRDeep2 - identifying miRNAs from deep sequencing data
microRNA
miRDeep2
updated 8 hours ago by
Ram
40k • written 10 hours ago by
Hasan
• 0
1
vote
4
replies
130
views
Unable to build applet in DNAnexus, .jar file not found
dnanexus
applet
updated 10 hours ago by
LChart
3.3k • written 14 hours ago by
_quantum_girl_
▴ 10
0
votes
1
reply
104
views
geom_signif() uses t-test to compare between more than 3 groups... Isn't this wrong?
ggplot2
ANOVA
t-test
updated 8 hours ago by
Ram
40k • written 11 hours ago by
RM123
• 0
0
votes
0
replies
61
views
Download an example of fully-imputed VCF files ?
VCF
impute
updated 8 hours ago by
Ram
40k • written 11 hours ago by
Ben
• 0
0
votes
1
reply
106
views
How to find the most representative protein data base ID for your protein?
modelling
protein
database
updated 11 hours ago by
GenoMax
134k • written 18 hours ago by
amy__
▴ 150
0
votes
2
replies
125
views
Visualize where kmers are on a reference genome
kmer
visualize
updated 13 hours ago by
Alex Reynolds
35k • written 14 hours ago by
Carrie
• 0
4
votes
5
replies
205
views
Filter human transcription factors
transcription-factor
RNA-seq
updated 7 hours ago by
Yogi
▴ 10 • written 13 hours ago by
Chris
▴ 180
2
votes
4
replies
157
views
obtaining circular RNAs' sequences from circBase
circular-RNA
8 hours ago by
aminijavad4
▴ 10
0
votes
0
replies
58
views
How to annotate BED for tissue expression?
BED
annotation
13 hours ago by
Fabio_bie88
• 0
2
votes
0
replies
77
views
Job:
Human Genomics Team Leader
ebi
ensembl
embl
genomics
14 hours ago by
Ben_Ensembl
★ 2.3k
0
votes
1
reply
1.7k
views
error when running local chlorop1.1
chlorop
updated 15 hours ago by
Ram
40k • written 7.3 years ago by
gerrychang1985
▴ 40
0
votes
1
reply
89
views
How to determine the total count for each gene in lymphotype B
scRNAseq
Seurat
updated 14 hours ago by
fracarb8
★ 1.2k • written 15 hours ago by
dalibenam64
• 0
3
votes
15
replies
1.8k
views
9 follow
Help writing code for a question on my homework
biopython
updated 16 hours ago by
Andreas
• 0 • written 2.4 years ago by
hannahcheyenna
• 0
1
vote
1
reply
186
views
bedGraph for Coverage of Insert from Paired-End Data?
genome
awk
coverage
bed
paired-end
updated 16 hours ago by
shelkmike
▴ 980 • written 3 days ago by
vanbelj
▴ 40
0
votes
1
reply
91
views
gene correlations in between two groups
gene-expression
correlation
updated 15 hours ago by
Ram
40k • written 16 hours ago by
edus_bioinfo
▴ 40
0
votes
1
reply
80
views
Running Ibex on both BCR chains?
BCR
ibex
single-cell
updated 15 hours ago by
Ram
40k • written 17 hours ago by
actinia94
• 0
1
vote
5
replies
226
views
Calculation of TMB on gene level
genomics
updated 39 minutes ago by
svp
▴ 580 • written 18 hours ago by
smrutimayipanda
▴ 20
0
votes
0
replies
66
views
Spike-in normalization in ATAC-Seq with DiffBind
ATAC-Seq
spike-in
DiffBind
18 hours ago by
frueher
• 0
0
votes
1
reply
205
views
News:
LAST CALL: Online Course - A Practical Introduction to NGS Data Analysis - October 23-25, 2023
DNA-seq
Workshop
RNA-seq
19 hours ago by
David Langenberger
10k
1
vote
2
replies
117
views
Is it normal if regress out the cell cycle effects but the DEGs are quite the similar (no big changes)
regress_out
Cell_cycle
Seurat
16 hours ago by
alwayshope
▴ 30
1
vote
8
replies
275
views
how to identify uniq genes between two gff files.
Genes
Uniq
Annotation
GFF
updated 9 hours ago by
Juke34
8.2k • written 22 hours ago by
nikhil
▴ 20
1
vote
3
replies
287
views
I have performed Trimmomatic run for adapter removal. QC report shows drop in the reads and presence of overrepresented sequences. Seeking help!
NGS
bioinformatics
illumina
WGS
updated 11 hours ago by
swbarnes2
13k • written 22 hours ago by
Vijith
▴ 30
0
votes
0
replies
83
views
filtering variants in a Strelka2 VCF file based on AD and AF
Filter
VCF
1 day ago by
Bogdan
★ 1.4k
5
votes
4
replies
242
views
Low Alignment rate
alignment
low_alignment_rate
Bowtie2
10 hours ago by
Mehwish
• 0
2
votes
4
replies
211
views
Integrated Seurat object change name of the two conditions
R
integrated
Seurat
13 hours ago by
camillab.
▴ 130
0
votes
4
replies
293
views
Hugo_Symbol to Entrez ID
hugo
bioinformatics
entrez
ids
symbols
updated 1 day ago by
Kevin Blighe
86k • written 3 days ago by
shakyaram079
• 0
2
votes
5
replies
257
views
How to change from gene_id to GeneID/EntrezID using R
identifiers
Deseq2
GeneID
updated 18 hours ago by
Kevin Blighe
86k • written 2 days ago by
Nicolas
• 0
0
votes
4
replies
700
views
Is there a way to get a list of all homogygous sites for each sample with plink (regardless if they are in a run)
plink
updated 1 day ago by
chrchang523
10k • written 16 days ago by
curious
▴ 730
1
vote
4
replies
209
views
How to sort cd-hit-est cluster file
sort
cd-hit-est
8 hours ago by
Mo
▴ 40
1
vote
4
replies
204
views
Enrichment of mitochondrial and ribosomal pathways - an artifact?
Pathway
Mitochondria
Ribosome
scRNA-seq
Enrichment
updated 4 hours ago by
LauferVA
3.7k • written 1 day ago by
omer.shomrat
• 0
13
votes
10
replies
591
views
8 follow
scRNAseq Differential expression analysis
scRNA-seq
Differential-Expression
Seurat
updated 22 hours ago by
ATpoint
76k • written 3 days ago by
MVJ
▴ 10
3
votes
4
replies
259
views
Dotplot : how to self-define the range of legend
analysis
seq
RNA
updated 15 hours ago by
GenoMax
134k • written 2 days ago by
Xuhao
• 0
0
votes
0
replies
94
views
News:
RADseq data analysis course
RADseq
Phylogenomics
Bioinformatics
Populationgenomics
Stacks
1 day ago by
carlopecoraro2
★ 2.3k
3
votes
2
replies
348
views
How to create structural variants ground truth for alignment of two long-read genome assemblies?
yeast
assembly
structural-variation
SV-callers
1 day ago by
Thomas
▴ 20
0
votes
0
replies
154
views
Merging the filename with tsv files for master file
genomics
2 days ago by
smrutimayipanda
▴ 20
1
vote
4
replies
260
views
Hisat2 index and alignment question
ubuntu
rna-seq
index
hisat2
1 day ago by
Athena
• 0
2
votes
4
replies
323
views
Ties in reranked list
fgsea
GSEA
2 days ago by
Hamza
• 0
1
vote
4
replies
325
views
Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempting To Use CuffDiff
CuffDiff
Bash
Cufflinks
2 days ago by
Y
• 0
0
votes
0
replies
133
views
My rMATS output file is not showing gene symbols and only XLOC gene ID are being shown.
rMATS
rMATS-turbo
2 days ago by
Nipan
• 0
112,641 results • Page
1 of 2253
Recent Votes
Comment: Calculation of TMB on gene level
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
Comment: ATAC-seq troubleshoot - Just Noise
t2t human reference genome for RNA-seq
Answer: Samtools Failing to Install through Conda
Answer: Importance of Data Structures for Bioinformatics?
Answer: Filter transcription factors
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Recent Replies
Answer: Can vg take MUMmer output as input?
by
Qi
• 0
get the sv from delta and u can set them as input of vg
Comment: Calculation of TMB on gene level
by
svp
▴ 580
TMB calculated by the number of non-synonymous somatic mutations per mega-base in coding regions. Performing TMB at gene level is technical…
Comment: ATAC-seq troubleshoot - Just Noise
by
vk
▴ 40
Do you think there's a possibility that something may have gone wrong in the sequencing step, as the bio-analyzer run seems to look okay or…
Answer: Samtools Failing to Install through Conda
by
hukai916
▴ 10
Same issue on brand new M2 chip MacBook: conda seems NOT able to find `samtools`; `brew` worked.
Comment: Enrichment of mitochondrial and ribosomal pathways - an artifact?
by
LauferVA
3.7k
im unclear on why you would ask this question without providing more context about the cell states that are being explored by the experimen…
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
by
Ram
40k
Singularity is a good option but OP explicitly mentions that their users are using their own laptops. On laptops, it's a lot easier to use …
Comment: Calculation of TMB on gene level
by
Zhenyu Zhang
▴ 980
It's what you asked for just mutation frequency or mutation frequency adjusted by gene length?
Comment: Understanding TCGA barcodes with dot in the fieldname
by
Zhenyu Zhang
▴ 980
second this. The "95FC84F5-4FB3-4CE7-ACD0-C7E0D8F03DD7" is obviously an UUID, not related to TCGA barcode
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
by
Yogi
▴ 10
Just 1 thing to consider. `Docker` is great because it provides a way to containerize applications. HOWEVER, many people on computation…
Comment: Filter human transcription factors
by
Yogi
▴ 10
Definitely the best resource. Was also going to recommend this one.
Comment: GO analysis after DESeq2
by
Ram
40k
The go category needs to be a [facet][1] on the ggplot. [1]: http://www.sthda.com/english/wiki/ggplot2-facet-split-a-plot-into-a-matrix-…
Comment: How to sort cd-hit-est cluster file
by
Mo
▴ 40
Hi, Thank you so much, this has worked :)
Comment: Program for Overlapping DMRs (Differentially Methylated Regions) Between Groups
by
LChart
3.3k
You might specify how the data is formatted. If you have `chr start end` columns, you can use `bedtools` to perform the interval operations.
Comment: RepeatMasker error when trying to generate repeat sequence distribution pie char
by
epianalysis
• 0
Do you mind telling me how you were able to create a custom txdb object that sufficiently annotates repeats?
Comment: obtaining circular RNAs' sequences from circBase
by
aminijavad4
▴ 10
I didn't know
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