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737 results • Page
3 of 15
Sort: Rank
Rank
Views
Votes
Replies
38
votes
21
replies
19k
views
8 follow
Tool:
pybam - 100% python BAM reader
python
htspython
bam
pysam
updated 11 months ago by
Ram
43k • written 8.1 years ago by
John
13k
76
votes
14
replies
13k
views
10 follow
Tool:
karyoploteR: uncircle your genomes
karyoploteR
Rdataviz
NGS
updated 11 months ago by
Ram
43k • written 7.0 years ago by
bernatgel
★ 3.4k
0
votes
0
replies
427
views
Tool:
Announcing the Papilloma Virus Episteme (PaVE) 2.0 Release
genomics
HPV
3D
2.1 years ago by
karlynn.noble
▴ 60
0
votes
0
replies
402
views
Tool:
Nature Communications: New AI tool for in-depth cleaning of a wide range of noise in single-cell RNA-Seq data
denoise
scRNA-Seq
AutoClass
AI
2.1 years ago by
bigmawen
▴ 430
9
votes
7
replies
1.7k
views
Tool:
miniDBG - a Jupyter notebook for teaching De Bruijn Graph assembly
python
deBruijnGraph
de_bruijn_graph
assembly
teaching
2.1 years ago by
Michael
54k
2
votes
0
replies
597
views
Tool:
Introducing ElasticBLAST – Run bigger BLAST searches faster on the Cloud
ElasticBLAST
BLAST
NCBI
updated 11 months ago by
Ram
43k • written 2.2 years ago by
PeterC_NCBI
▴ 410
1
vote
1
reply
614
views
Tool:
New VCF Header (schema) Parser---Please Break!!!
VCF
header
updated 2.2 years ago by
d-cameron
★ 2.9k • written 2.2 years ago by
ariel
▴ 250
231
votes
38
replies
146k
views
29 follow
Tool:
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
ensembl
genome-coordinates
liftover
updated 11 months ago by
Ram
43k • written 11.2 years ago by
Malachi Griffith
20k
5
votes
2
replies
2.4k
views
Tool:
eLabFTW: a free and open source electronic lab notebook
elabftw
free-open-source-software
php
updated 11 months ago by
Ram
43k • written 4.7 years ago by
Nico
▴ 190
1
vote
1
reply
3.7k
views
Tool:
mirDIP 4.1 - integrative database of human microRNA target predictions
interactome
miRNA
targets
microRNA
updated 11 months ago by
Ram
43k • written 6.0 years ago by
tomastokar
▴ 50
2
votes
6
replies
3.4k
views
Tool:
microbiomeMarker: microbiome biomarker analysis in R
stamp
microbiome
lefse
updated 11 months ago by
Ram
43k • written 3.9 years ago by
yiluheihei
▴ 30
5
votes
8
replies
7.1k
views
6 follow
Tool:
Converting MUMmer snps file to a real VCF file
VCF
mummer
SNP
updated 11 months ago by
Ram
43k • written 4.8 years ago by
Matteo Schiavinato
★ 3.6k
4
votes
3
replies
1.2k
views
Tool:
Make a Sequence Logo in your browser by using native Javascript.
javascript
sequence
browser
logo
2.3 years ago by
Paul A. Gagniuc
▴ 30
0
votes
0
replies
470
views
Tool:
Local sequence alignment made visual in your browser
javascript
browser
sequence
alignment
local
2.2 years ago by
Paul A. Gagniuc
▴ 30
15
votes
11
replies
8.3k
views
Tool:
Arriba: Fast and accurate gene fusion detection from RNA-Seq data
variant-calling
RNA-Seq
cancer
gene-fusion
updated 11 months ago by
Ram
43k • written 6.3 years ago by
uhrigs
▴ 150
0
votes
0
replies
483
views
Tool:
AIQC - open source framework making deep learning accessible for researchers.
statistics
machine
multi-omic
learning
ai
2.4 years ago by
Kermit
▴ 90
28
votes
17
replies
5.1k
views
7 follow
Tool:
PCAtools: everything Principal Components Analysis
eigenvector
pca
bioconductor
R
updated 11 months ago by
Ram
43k • written 5.3 years ago by
Kevin Blighe
88k
13
votes
7
replies
4.2k
views
Tool:
I-PV: a CIRCOS module for interactive protein sequence visualization
interactive
javascript
circos
sequence
updated 21 months ago by
Ram
43k • written 8.6 years ago by
Ibrahim Tanyalcin
★ 1.2k
0
votes
1
reply
689
views
Tool:
Molecular Dynamics analysis tools [desmond Schrodinger]
dynamics
schrodinger
desmond
mdanalysis
molecular
updated 2.5 years ago by
GenoMax
142k • written 2.5 years ago by
tLaw
• 0
0
votes
0
replies
519
views
Tool:
SBGNview published online with Bioinformatics
Pathview
BioConductor
SBNGview
visualization
pathway
2.5 years ago by
bigmawen
▴ 430
10
votes
5
replies
2.5k
views
Tool:
Genozip: A new compression tool for FASTQ, BAM, VCF and more
bam
vcf
fastq
compression
10 months ago by
Divon
▴ 230
0
votes
0
replies
444
views
Tool:
Proteome-pI 2.0 - Proteome Isoelectric Point Database
isoelectric_point
protein
pKa
database
proteomics
2.5 years ago by
Lukasz Kozlowski
• 0
4
votes
13
replies
2.8k
views
Tool:
SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
pathway-analysis
visualization
Pathview
SBGN
updated 11 months ago by
Ram
43k • written 3.2 years ago by
bigmawen
▴ 430
1
vote
1
reply
924
views
Tool:
Cell Type Prediction - covering 45 immune cell types
citeseq
scRNA
singlecell
updated 2.6 years ago by
Igor
▴ 50 • written 2.7 years ago by
sonpham
▴ 580
3
votes
5
replies
2.8k
views
Tool:
Extend 3' UTR of a GTF file
annotation
python
RNA-Seq
GTF
updated 11 months ago by
Ram
43k • written 3.6 years ago by
Shred
★ 1.4k
10
votes
1
reply
1.5k
views
Tool:
fastp 0.23.0 released, runs 2x faster, and generates reproducible outputs.
FASTQ
updated 2.6 years ago by
GenoMax
142k • written 2.6 years ago by
chen
★ 2.5k
1
vote
0
replies
602
views
Tool:
A pairwise genome alignment pipeline using LAST and Nextflow
genome
LAST
Nextflow
dotplot
alignment
2.6 years ago by
Charles Plessy
★ 2.9k
0
votes
0
replies
590
views
Tool:
NGS-Barcode-Count
DEL
NGS
CRISPRseq
2.6 years ago by
coffeyrt
• 0
0
votes
0
replies
1.3k
views
Tool:
Utilising QIIME 2 pipeline: a current and future golden standard platform to analyze Amplicon-Seq data
NGS
Sequencing
updated 15 months ago by
Ram
43k • written 2.6 years ago by
Novogene
▴ 420
4
votes
0
replies
735
views
Tool:
Annoyed by contig name inconsistencies (eg chr22 vs 22)? A solution
contigs
bam
vcf
reference
compression
2.7 years ago by
Divon
▴ 230
0
votes
0
replies
689
views
Tool:
Genotype Imputation Workflow
gwas
imputation.
2.7 years ago by
nhaus
▴ 360
1
vote
0
replies
498
views
Tool:
shell script to search txt in academic figures
search_txt_in_image.sh
2.7 years ago by
Zhilong Jia
★ 2.2k
0
votes
0
replies
1.1k
views
Tool:
Still Not Use QIIME2 for Amplicon Analysis? You’re OUT!
NGS
Sequencing
updated 15 months ago by
Ram
43k • written 2.7 years ago by
Novogene
▴ 420
1
vote
2
replies
989
views
Tool:
krust: a k-mer counter in Rust using the rust-bio and rayon crates
Rust
kmer-counting
fasta
kmer
updated 2.7 years ago by
Istvan Albert
100k • written 2.7 years ago by
jlivesey
▴ 10
0
votes
1
reply
1.1k
views
Tool:
BioFileConverter - an app for Mac users to convert .xdna and .dna files into genbank .gb files and more
dna
genbank
xdna
updated 14 months ago by
Ram
43k • written 2.7 years ago by
vytarasov
▴ 180
4
votes
3
replies
1.4k
views
Tool:
brename: safely batch renaming files/directories via regular expression
batch
renaming
updated 2.7 years ago by
Ram
43k • written 2.7 years ago by
shenwei356
8.5k
0
votes
0
replies
1.2k
views
Tool:
Handy online tool for genomic analysis and data visualization - Part II
NGS
Sequencing
updated 14 months ago by
Ram
43k • written 2.7 years ago by
Novogene
▴ 420
1
vote
0
replies
521
views
Tool:
Looking for feedback on epigenetics R package - enhancer detection and visualization
epigenetics
chromatin
enhancers
atac
chip
2.7 years ago by
Alex
▴ 20
0
votes
0
replies
564
views
Tool:
A framework to prioritize miRNA-driven post-transcriptional signals using exonic and intronic regions of RNAseq data
post-transcriptional
miRNA
intron
exon
RNAseq
2.7 years ago by
Emilio Marmol
▴ 170
50
votes
16
replies
14k
views
12 follow
Tool:
Omictools: A didactic directory for omic data analysis (NGS, microarray, PCR, MS, NMR)
pcr
software
ngs
updated 11 months ago by
Ram
43k • written 10.7 years ago by
arnaud.desfeux
▴ 450
1
vote
0
replies
584
views
Tool:
Omics Playground: visualization and analysis of transcriptomics and proteomics data
proteomics
RNA
RNA-seq
scRNA-seq
omics
data
2.8 years ago by
bigomics.team
▴ 90
2
votes
2
replies
1.0k
views
Tool:
miRAnno—network-based functional microRNA annotation
pathways
miRNA
annotation
microRNA
2.8 years ago by
tomastokar
▴ 50
21
votes
14
replies
9.5k
views
Tool:
trackplot: Fast and minimal dependency standalone R script to generate IGV style locus tracks from bigWig files
visualization
igv
ChIP-Seq
R
bigwigs
updated 11 months ago by
Ram
43k • written 3.5 years ago by
poisonAlien
★ 3.2k
1
vote
0
replies
2.0k
views
Tool:
Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
biomart
annotation
Ensembl
2.8 years ago by
Shred
★ 1.4k
1
vote
0
replies
557
views
Tool:
BIRCH Bioinformatics System v3.80
alignment
RNA-seq
genome
assembly
sequence
phylogeny
2.8 years ago by
brian.fristensky
▴ 460
0
votes
0
replies
591
views
Tool:
Manticore: a software to extract the intermixed regions of subgenomes in hybrid species
mapping
hybrid
subgenome
genomics
sequencing
2.8 years ago by
Matteo Schiavinato
★ 3.6k
3
votes
1
reply
1.2k
views
Tool:
all2vcf: a tool to convert non-standard variant outputs (mummer. bcftools isec) to VCF
mummer
isec
variant
bcftools
VCF
updated 19 months ago by
ayeshatariq78
• 0 • written 2.8 years ago by
Matteo Schiavinato
★ 3.6k
0
votes
0
replies
999
views
Tool:
Handy online tool for genomic analysis and data visualization - Part I
NGS
Sequencing
updated 14 months ago by
Ram
43k • written 2.8 years ago by
Novogene
▴ 420
2
votes
0
replies
669
views
Tool:
metaGEM: create your own genome scale metabolic models directly from metagenomes
metagenomics
metagenome-assembled-genome
genome-scale-metabolic-model
metabolism
updated 2.8 years ago by
Ram
43k • written 2.8 years ago by
metagenomez
▴ 20
9
votes
7
replies
3.0k
views
Tool:
DiffBind 3.0: Extensive updates in Bioconductor 3.12
DiffBind
ChIP-Seq
diffbind
ATAC-seq
chipseq
updated 11 months ago by
Ram
43k • written 3.6 years ago by
Rory Stark
★ 2.0k
737 results • Page
3 of 15
Recent Votes
Answer: Filter Genome for Specific Sites
Answer: Filter Genome for Specific Sites
Answer: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
The Biostar Herald for Monday, May 20, 2024
Answer: Generating Group/Cluster Lists from fastq files
The Biostar Herald for Monday, May 20, 2024
ClusterProfiler : What is GeneRatio and BgRatio?
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Comment: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
by
GenoMax
142k
For those samples it appears that raw data was not submitted. Just an assembly. $ esearch -db biosample -query SAMN08009548 | elink -…
Comment: How can I calculate the OS of each patient?
by
Pedro
• 0
**I have already tried this code. listSamples with HNSC cancer and smokers. I need at least one supporting material to find out the survi…
Comment: Filter Genome for Specific Sites
by
Anita
• 0
Great, thank you!
Comment: Filter Genome for Specific Sites
by
Anita
• 0
This is unhelpful and doesn't answer my question.
Comment: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
by
Harshita
• 0
It seems that the authors in this paper have used paired-end sequences only for their analysis, and for that, they would also have used the…
Comment: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
by
Harshita
• 0
Thank you so much for helping me out in this! I have used most of the sequences that are found in this table. But, some samples like the…
Answer: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
by
GenoMax
142k
Looks like the samples are from this project: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA320483&o=acc_s%3Aa This table has the SR…
Comment: Filter Genome for Specific Sites
by
Pierre Lindenbaum
161k
> My sites are in an Excel file right now ![enter image description here][1] <!-- was an American educator and academic administrator…
Answer: Filter Genome for Specific Sites
by
GenoMax
142k
> I have a list of ~1,300 single bp sites Convert your file to plain text [**BED format**][1] (three fields required). Use `bedtools slo…
Comment: How to generate an Upset plot in R to plot the shared variants between cell free
by
sainavyav22
• 0
It worked, Thank you very much!
Comment: What marks a De-Novo Genome assembly as FAILED?
by
dthorbur
★ 2.0k
I'm unsure you'll be able to identify whole chromosomes that are not core from illumina reads alone. That might be easier to do with a micr…
Comment: Error in using BioSampleParser tool: subscript out of bounds
by
Mohamed Samir
▴ 20
Dear marco, We need to ask ourselves why it is not working for all bioprojects ? I have looked into this, and observed that as long as the…
Comment: Why most genes have high padj values
by
Ram
43k
You ***want*** ~3000 DE genes?<a href="" title="Text added because biostars parser needs it"></a>
Answer: Generating Group/Cluster Lists from fastq files
by
GenoMax
142k
> I was hoping to just do this in galaxy This is not a galaxy option but `clumpify.sh ` from BBMap suite can cluster sequences/dedupe th…
Comment: Practical Haplotype Graph v2 not finding correct paths
by
beantkapoor16
▴ 10
Hello, just wanted to check in if the code has been fixed yet? Thank you.
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