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670 results • Page
1 of 14
Sort: Rank
Rank
Views
Votes
Replies
2
votes
0
replies
44
views
Tool:
Efficient querying of genomic reference databases with gget
ensembl
5 hours ago by
Laura
▴ 20
1
vote
4
replies
162
views
Tool:
Quick Command to Filter Bam Files
bed
awk
1 day ago by
Sasha
• 0
2
votes
0
replies
101
views
Tool:
OakVar: genomic variant analysis tool
genomics
variant
bioinformatics
4 days ago by
Ryangguk Kim
▴ 80
26
votes
4
replies
12k
views
Tool:
Plotting GSEA output in R
javaGSEA
GSEA
RNA-Seq
plot
Tool
updated 4 days ago by
valentinafu
• 0 • written 5.8 years ago by
thomaskuilman
▴ 820
25
votes
19
replies
5.9k
views
10 follow
Tool:
pathfindR - Enrichment Analysis using Active Subnetworks
enrichment
pathway
active
subnetwork
R
Tool
updated 12 days ago by
Deepblue
▴ 10 • written 4.2 years ago by
egeulgen
★ 1.2k
1
vote
1
reply
211
views
Tool:
Roakvar: do genomic variant analyses with R
oakvar
genomics
roakvar
variant
analysis
updated 14 days ago by
cpad0112
20k • written 14 days ago by
Ryangguk Kim
▴ 80
16
votes
3
replies
9.4k
views
Tool:
Vcflib Documentation
vcf
Tool
updated 24 days ago by
DrN
• 0 • written 9.2 years ago by
Erik Garrison
★ 2.3k
38
votes
21
replies
14k
views
8 follow
Tool:
pybam - 100% python BAM reader
python
bam
pysam
htspython
Tool
updated 4 weeks ago by
Niveditha
• 0 • written 6.1 years ago by
John
13k
71
votes
14
replies
9.5k
views
10 follow
Tool:
karyoploteR: uncircle your genomes
R
Tool
dataviz
karyoploteR
NGS
updated 4 weeks ago by
Midge
• 0 • written 5.0 years ago by
bernatgel
★ 3.3k
0
votes
0
replies
89
views
Tool:
Announcing the Papilloma Virus Episteme (PaVE) 2.0 Release
genomics
HPV
3D
5 weeks ago by
karlynn.noble
▴ 60
0
votes
0
replies
93
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
6 weeks ago by
bigmawen
▴ 430
9
votes
7
replies
556
views
Tool:
miniDBG - a Jupyter notebook for teaching De Bruijn Graph assembly
python
deBruijnGraph
de_bruijn_graph
assembly
teaching
4 weeks ago by
Michael Dondrup
51k
2
votes
0
replies
167
views
Tool:
Introducing ElasticBLAST – Run bigger BLAST searches faster on the Cloud
Tool
NCBI
BLAST
ElasticBLAST
9 weeks ago by
PeterC_NCBI
▴ 20
1
vote
1
reply
203
views
Tool:
New VCF Header (schema) Parser---Please Break!!!
VCF
header
updated 10 weeks ago by
d-cameron
★ 2.6k • written 10 weeks ago by
ariel
▴ 190
215
votes
36
replies
125k
views
27 follow
Tool:
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
genome
coordinates
conversion
liftover
ensembl
Tool
updated 11 weeks ago by
jena
▴ 170 • written 9.2 years ago by
Malachi Griffith
19k
5
votes
2
replies
1.8k
views
Tool:
eLabFTW: a free and open source electronic lab notebook
software
open-source
free
php
Tool
3 months ago by
Nico
▴ 190
1
vote
1
reply
2.9k
views
Tool:
mirDIP 4.1 - integrative database of human microRNA target predictions
microRNA
miRNA
tool
interactome
targets
Tool
updated 3 months ago by
Dana
• 0 • written 4.0 years ago by
tomastokar
▴ 50
9
votes
20
replies
6.9k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
Tool
software
3 months ago by
vytarasov
▴ 160
2
votes
6
replies
2.1k
views
Tool:
microbiomeMarker: microbiome biomarker analysis in R
microbiome
lefse
Tool
stamp
updated 3 months ago by
MSRS
▴ 540 • written 23 months ago by
yiluheihei
▴ 30
5
votes
8
replies
4.0k
views
6 follow
Tool:
Converting MUMmer snps file to a real VCF file
mummer
SNP
Tool
conversion
VCF
updated 3 months ago by
Alish
• 0 • written 2.8 years ago by
Macspider
★ 3.5k
5
votes
3
replies
501
views
Tool:
Make a Sequence Logo in your browser by using native Javascript.
javascript
sequence
browser
logo
4 months ago by
Paul A. Gagniuc
▴ 40
0
votes
0
replies
148
views
Tool:
Local sequence alignment made visual in your browser
javascript
browser
sequence
alignment
local
3 months ago by
Paul A. Gagniuc
▴ 40
15
votes
11
replies
6.3k
views
Tool:
Arriba: Fast and accurate gene fusion detection from RNA-Seq data
RNA-Seq
cancer
variant calling
gene
fusion
Tool
4 months ago by
uhrigs
▴ 150
0
votes
0
replies
154
views
Tool:
AIQC - open source framework making deep learning accessible for researchers.
statistics
machine
multi-omic
learning
ai
4 months ago by
syntax
▴ 60
28
votes
17
replies
3.2k
views
7 follow
Tool:
PCAtools: everything Principal Components Analysis
pca
eigenvector
R
bioconductor
Tool
updated 4 months ago by
annamariabugaj
• 0 • written 3.3 years ago by
Kevin Blighe
81k
13
votes
7
replies
3.3k
views
Tool:
I-PV: a CIRCOS module for interactive protein sequence visualization
circos
interactive
sequence
javascript
Tool
5 months ago by
Ibrahim Tanyalcin
★ 1.2k
0
votes
1
reply
260
views
Tool:
Molecular Dynamics analysis tools [desmond Schrodinger]
dynamics
schrodinger
desmond
mdanalysis
molecular
updated 6 months ago by
GenoMax
115k • written 6 months ago by
tLaw
• 0
0
votes
0
replies
193
views
Tool:
SBGNview published online with Bioinformatics
Pathview
BioConductor
SBNGview
visualization
pathway
6 months ago by
bigmawen
▴ 430
9
votes
5
replies
1.1k
views
Tool:
Genozip: A new compression tool for FASTQ, BAM, VCF and more
bam
vcf
fastq
compression
5 months ago by
Divon
▴ 180
0
votes
0
replies
178
views
Tool:
Proteome-pI 2.0 - Proteome Isoelectric Point Database
isoelectric_point
protein
pKa
database
proteomics
6 months ago by
Lukasz Kozlowski
• 0
4
votes
13
replies
1.4k
views
Tool:
SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
Pathview
SBGN
pathway analysis
visualization
Tool
updated 7 months ago by
neha.ghevaria3
• 0 • written 15 months ago by
bigmawen
▴ 430
1
vote
1
reply
418
views
Tool:
Cell Type Prediction - covering 45 immune cell types
citeseq
scRNA
singlecell
updated 7 months ago by
Igor
▴ 40 • written 9 months ago by
sonpham
▴ 580
3
votes
5
replies
1.3k
views
Tool:
Extend 3' UTR of a GTF file
RNA-Seq
annotation
GTF
python
Tool
updated 7 months ago by
Dylan
• 0 • written 20 months ago by
Shred
▴ 620
10
votes
1
reply
700
views
Tool:
fastp 0.23.0 released, runs 2x faster, and generates reproducible outputs.
FASTQ
updated 7 months ago by
GenoMax
115k • written 7 months ago by
chen
★ 2.4k
1
vote
0
replies
233
views
Tool:
A pairwise genome alignment pipeline using LAST and Nextflow
genome
LAST
Nextflow
dotplot
alignment
8 months ago by
Charles Plessy
★ 2.8k
0
votes
0
replies
248
views
Tool:
NGS-Barcode-Count
DEL
NGS
CRISPRseq
8 months ago by
coffeyrt
• 0
0
votes
0
replies
384
views
Tool:
Utilising QIIME 2 pipeline: a current and future golden standard platform to analyze Amplicon-Seq data
Bioinformatics
NGS
Sequencing
BI
8 months ago by
Novogene
▴ 160
4
votes
0
replies
299
views
Tool:
Annoyed by contig name inconsistencies (eg chr22 vs 22)? A solution
contigs
bam
vcf
reference
compression
8 months ago by
Divon
▴ 180
0
votes
0
replies
280
views
Tool:
Genotype Imputation Workflow
gwas
imputation.
8 months ago by
nhaus
▴ 200
1
vote
0
replies
217
views
Tool:
shell script to search txt in academic figures
search_txt_in_image.sh
8 months ago by
Zhilong Jia
★ 2.1k
0
votes
0
replies
492
views
Tool:
Still Not Use QIIME2 for Amplicon Analysis? You’re OUT!
NGS
analysis
BI
Bioinformatics
Sequencing
8 months ago by
Novogene
▴ 160
1
vote
2
replies
501
views
Tool:
krust: a k-mer counter in Rust using the rust-bio and rayon crates
Rust
kmer-counting
fasta
kmer
updated 8 months ago by
Istvan Albert
93k • written 8 months ago by
jlivesey
▴ 10
0
votes
1
reply
508
views
Tool:
BioFileConverter - an app for Mac users to convert .xdna and .dna files into genbank .gb files and more
xdna
file
gb
dna
genbank
8 months ago by
vytarasov
▴ 160
3
votes
3
replies
620
views
Tool:
brename: safely batch renaming files/directories via regular expression
batch
renaming
updated 8 months ago by
Ram
36k • written 8 months ago by
shenwei356
7.1k
0
votes
0
replies
363
views
Tool:
Handy online tool for genomic analysis and data visualization - Part II
NGS
analysis
BI
Bioinformatics
Sequencing
updated 9 months ago by
cpad0112
20k • written 9 months ago by
Novogene
▴ 160
1
vote
0
replies
246
views
Tool:
Looking for feedback on epigenetics R package - enhancer detection and visualization
epigenetics
chromatin
enhancers
atac
chip
9 months ago by
Alex
▴ 20
0
votes
0
replies
258
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
9 months ago by
Emilio Marmol
▴ 150
50
votes
16
replies
12k
views
12 follow
Tool:
Omictools: A didactic directory for omic data analysis (NGS, microarray, PCR, MS, NMR)
pcr
Tool
software
ngs
updated 8 months ago by
Ram
36k • written 8.7 years ago by
arnaud.desfeux
▴ 450
1
vote
0
replies
278
views
Tool:
Omics Playground: visualization and analysis of transcriptomics and proteomics data
proteomics
RNA
RNA-seq
scRNA-seq
omics
data
10 months ago by
bigomics.team
▴ 90
2
votes
2
replies
487
views
Tool:
miRAnno—network-based functional microRNA annotation
pathways
miRNA
annotation
microRNA
10 months ago by
tomastokar
▴ 50
670 results • Page
1 of 14
Recent Votes
C: PI_HAT and Z-values for relationships (PLINK IBD calculation)
Efficient querying of genomic reference databases with gget
Integrating VDJ sequencing data with Seurat
Efficient querying of genomic reference databases with gget
Comment: how to fetch intron coordinates from transcriptome.gtf file ? is there any dir
A: Regression using genotype on expression of genes
A: How to use ALLPATH-LG assembler
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Popular Question
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I0110
▴ 120
Popular Question
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always_learning
★ 1.1k
Teacher
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h.mon
34k
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▴ 60
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Recent Replies
Answer: enrichr
by
Laura
▴ 20
Use it through [gget enrichr][1] for super easy use! [1]: https://github.com/pachterlab/gget
Comment: DESeq2 use of factors for colData
by
swbarnes2
12k
I believe it will try to make a linear correlation between the logs of the counts and your numerical colData. But it's hard to know withou…
Comment: Difference in total gene counts between samples
by
swbarnes2
12k
I think it's glaringly obvious that library size is driving your first PC. I would not be at all confident that the typical techniques wil…
Answer: Retrieving ensembl protein length with biomart
by
Laura
▴ 20
*[gget][1] seq* will return the nucleotide (option "gene") or amino acid (option "transcript") sequence and sequence length for any Ensembl…
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
by
Pierre Lindenbaum
145k
`$1`: https://www.gnu.org/software/gawk/manual/gawk.html#Fields `/^@/`: https://www.gnu.org/software/gawk/manual/gawk.html#Regexp-Usage `…
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
by
I0110
▴ 120
What is the "$1 ~ /^@/'" part for? Thanks!
Answer: fastq.gz download error
by
GenoMax
115k
This dataset appears to have been released just a few days back (20th May) so it may not be fully ready to download from ENA. $ curl …
Comment: fastq.gz download error
by
nishimalhotra2612
▴ 10
I m downloading it directly from ENA database Generated fastq files:FTP And the operating system is windows 11 It's not the error but …
Comment: fastq.gz download error
by
lieven.sterck
13k
you'll need to provide some more (crucial) information here: how are you downloading it? (program? OS?) , what is the error you get? ... th…
Comment: snakemake r script
by
nishimalhotra2612
▴ 10
thanks i will modify script and will install the needed package
Comment: snakemake r script
by
nishimalhotra2612
▴ 10
thank you so much
Comment: Third Quartile (Q3) for RNAseq data
by
Leo
• 0
I read that it is a common approach to use ConsensusClusterPlus. I am trying to figure out, are TCGA data_mrna_seq_v2_rsem.txt data already…
Comment: how to fetch intron coordinates from transcriptome.gtf file ? is there any dir
by
ATpoint
61k
Indeed, good catch!
Comment: how to fetch intron coordinates from transcriptome.gtf file ? is there any dir
by
rpolicastro
8.2k
If you want the exact intron ranges you would need to modify the above but by looking per transcript. Doing it per gene would give you regi…
Comment: PCA plot interpretation after accounting for batch effects with SVA
by
rpolicastro
8.2k
There doesn't appear to be an appreciable separation between the two conditions for most of your samples. Instead of immediately going to S…
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