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733 results • Page
2 of 15
Sort: Rank
Rank
Views
Votes
Replies
362
votes
82
replies
144k
views
35 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel
next-gen
ngs
updated 5 weeks ago by
jena
▴ 290 • written 11.2 years ago by
ole.tange
★ 4.4k
0
votes
0
replies
3.3k
views
Tool:
euka: Robust detection of eukaryotic taxa from modern and ancient environmental DNA using pangenomic reference graphs.
pangenomics
vg
sedaDNA
graph
environmental-DNA
updated 12 months ago by
Ram
43k • written 12 months ago by
Nicola
▴ 10
0
votes
1
reply
434
views
Tool:
TRcaller : a novel Tool for SSR /STR/TR genotyping from NGS data for short and long reads
SSR
NGS
genotype
STR
updated 12 months ago by
Ram
43k • written 12 months ago by
Xuewen
• 0
46
votes
9
replies
43k
views
7 follow
Tool:
Tools to merge overlapping paired-end reads
ngs
Assembly
fastq
updated 12 months ago by
Charles-Alexandre Roy
▴ 50 • written 7.4 years ago by
Abdul Rafay Khan
★ 1.2k
4
votes
0
replies
882
views
Tool:
PyComplexHeatmap: a Python package to visualize multimodal genomics data
visualization
Python
ComplexHeatmap
PyComplexHeatmap
23 days ago by
Wubin
▴ 40
0
votes
0
replies
361
views
Tool:
BioLabImage - Mac program for DNA/RNA/protein gel/blot, cells/colonies image analysis
image-analysis
gel
blot
cells
colonies
updated 13 months ago by
Ram
43k • written 13 months ago by
vytarasov
▴ 180
6
votes
10
replies
4.6k
views
Tool:
Giant Virus Finder - discover giant virus sequences in metagenomes
Giant-Virus-Finder
updated 13 months ago by
Ram
43k • written 8.2 years ago by
Csaba Kerepesi
▴ 350
2
votes
2
replies
810
views
Tool:
NCBI's Foreign Contamination Screen (FCS) tool improves the quality of GenBank submissions
NCBI
Submission
GenBank
13 months ago by
PeterC_NCBI
▴ 410
1
vote
0
replies
681
views
Tool:
BioLabDNA - Mac program for DNA analysis and cloning.
cloning
DNA
protein
alignment
assembly
13 months ago by
vytarasov
▴ 180
1
vote
0
replies
439
views
Tool:
FungiExpresZ: an intuitive package for fungal gene expression data analysis, visualization and discovery
r
gene-expression
RNA-seq
fungi
updated 14 months ago by
Ram
43k • written 14 months ago by
Chirag Parsania
★ 2.0k
0
votes
0
replies
480
views
Tool:
GraphBio: A shiny web app to easily perform popular visualization analysis for omics data
visualization
heatmap
volcano-plot
updated 14 months ago by
Ram
43k • written 14 months ago by
Shuzhi
• 0
1
vote
0
replies
446
views
Tool:
HaploCart: Human mtDNA Haplogroup Classification Using a Pangenomic Reference Graph
graph
human
pangenome
haplogroup
mitochondrion
14 months ago by
Gabriel R.
★ 2.9k
5
votes
0
replies
750
views
Tool:
BAM index visualizer - a tool for helping to understand the BAI file format
bam
15 months ago by
cmdcolin
★ 3.8k
9
votes
22
replies
9.7k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
10 months ago by
vytarasov
▴ 180
2
votes
0
replies
460
views
Tool:
GeneWarrior is now open source
open
source
16 months ago by
r.follador
▴ 90
0
votes
0
replies
608
views
Tool:
split pooled paired-end fastq using fqkit
fastq
split
barcode
updated 16 months ago by
GenoMax
142k • written 16 months ago by
size_t
▴ 120
1
vote
0
replies
780
views
Tool:
Mabs, a parameter optimizer for Hifiasm and Flye
assembly
7 months ago by
shelkmike
★ 1.2k
1
vote
2
replies
713
views
Tool:
UUIDtoBarcode Renaming of Folders
UUIDtoBarcode
R
updated 16 months ago by
Zhenyu Zhang
★ 1.2k • written 16 months ago by
Kaia
▴ 10
4
votes
0
replies
541
views
Tool:
Visual analysis of VCF files
vcf
visual-analysis
updated 17 months ago by
Ram
43k • written 17 months ago by
cocchi.e89
▴ 270
1
vote
0
replies
451
views
Tool:
BioIllustrator - Mac program for the creation of illustrations for scientific articles
molecular
cell
biology
scientific
illustration
17 months ago by
vytarasov
▴ 180
2
votes
4
replies
1.0k
views
Tool:
Tool: Quick Command To Change BED file Naming Convention
bed
awk
updated 5 months ago by
mavy
▴ 10 • written 17 months ago by
Sasha
▴ 840
4
votes
2
replies
2.6k
views
Tool:
pyMSAviz - MSA visualization python package for sequence analysis
visualization
MSA
Python
updated 17 months ago by
Wayne
★ 2.0k • written 17 months ago by
moshi
▴ 150
4
votes
2
replies
1.2k
views
Tool:
Introducing Cramino: a *fast* QC tool for long reads
long-read
nanopore
pacbio
updated 28 days ago by
Ram
43k • written 18 months ago by
WouterDeCoster
47k
1
vote
1
reply
529
views
Tool:
trackBrowser: Visualization of sequencing data within a given genome region
RNA
browser
modification
updated 18 months ago by
Alex Reynolds
35k • written 18 months ago by
lsp03yjh
▴ 860
3
votes
1
reply
857
views
Tool:
The Encyclopedia of RNA Epitranscriptome : decoding the mechanisms and functions of diverse RNA modifications
m6A
m1A
m5C
modification
epitranscriptome
18 months ago by
lsp03yjh
▴ 860
4
votes
2
replies
727
views
Tool:
Rethinking containers for cloud native pipelines
workflow
container
pipeline
nextflow
18 months ago by
Marcel Ribeiro-Dantas
▴ 470
2
votes
0
replies
833
views
Tool:
Query and annotate variants with gnomAD python
sql
disease
variants
python
gnomad
18 months ago by
Kalin
▴ 50
0
votes
0
replies
348
views
Tool:
Binding free energy
Binding-free-energy
MD-simulation
updated 16 months ago by
Ram
43k • written 18 months ago by
gustmarq4
• 0
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
1
vote
2
replies
633
views
Tool:
Easy phylogenomics by BuscoPhylo
Phylogenomics
20 months ago by
slimane.khayi
▴ 80
0
votes
0
replies
559
views
Tool:
CZ CELLxGENE - Single-cell visualization and analysis tool
visualization
scRNA-seq
rna-seq
updated 11 months ago by
Ram
43k • written 20 months ago by
mczerwinski
▴ 40
2
votes
1
reply
658
views
Tool:
Best-practice bulk RNA-seq workflow with citations
rnaseq
sequencing
bulkrnaseq
rna
updated 21 months ago by
Kenny
▴ 30 • written 21 months ago by
Kenny
▴ 20
2
votes
0
replies
481
views
Tool:
NCBI's BLAST ClusteredNR database results have in-cluster analysis
BLAST
NCBI
ClustereedNR
21 months ago by
PeterC_NCBI
▴ 410
1
vote
0
replies
479
views
Tool:
Briefings in Bioinformatics: Hiplot visualization toolkit
data-mining
visualization
updated 21 months ago by
Ram
43k • written 22 months ago by
Jianfeng
▴ 10
2
votes
1
reply
735
views
Tool:
NCBI IgBLAST release 1.19.0 for immunoglobulin and T cell receptor variable domain sequences now available
BLAST
IgBLAST
NCBI
updated 22 months ago by
Jesse
▴ 740 • written 22 months ago by
PeterC_NCBI
▴ 410
2
votes
5
replies
972
views
Tool:
Latest release of NCBI Magic-BLAST now available
BLAST
NCBI
Magic-BLAST
updated 21 months ago by
GenoMax
142k • written 22 months ago by
PeterC_NCBI
▴ 410
4
votes
0
replies
679
views
Tool:
Single Cell Portal - a free and open platform for viewing, sharing and interacting with single cell genomic data
gene-expression
scrna-seq
single-cell
visualization
22 months ago by
Single Cell Portal
▴ 40
1
vote
2
replies
884
views
Tool:
Roakvar: do genomic variant analyses with R
oakvar
genomics
roakvar
variant
analysis
23 months ago by
Ryangguk Kim
▴ 90
3
votes
1
reply
966
views
Tool:
OakVar: genomic variant analysis tool
genomics
variant
updated 16 months ago by
Ram
43k • written 23 months ago by
Ryangguk Kim
▴ 90
27
votes
5
replies
1.9k
views
6 follow
Tool:
Efficient querying of genomic reference databases with gget
ensembl
enrichr
ncbi
gget
uniprot
updated 23 months ago by
Lior Pachter
▴ 700 • written 23 months ago by
Laura Luebbert
▴ 450
0
votes
0
replies
445
views
Tool:
BIRCH Bioinformatics System v3.86
genomics
sequence
blast
transcriptomics
23 months ago by
brian.fristensky
▴ 460
1
vote
4
replies
818
views
Tool:
Quick Command to Filter Bam Files
bed
awk
23 months ago by
Sasha
▴ 840
28
votes
4
replies
15k
views
Tool:
Plotting GSEA output in R
RNA-Seq
javaGSEA
GSEA
updated 10 months ago by
Ram
43k • written 7.7 years ago by
thomaskuilman
▴ 850
25
votes
19
replies
8.2k
views
10 follow
Tool:
pathfindR - Enrichment Analysis using Active Subnetworks
subnetwork
R
pathway-enrichment
updated 10 months ago by
Ram
43k • written 6.2 years ago by
egeulgen
★ 1.3k
16
votes
3
replies
11k
views
Tool:
Vcflib Documentation
vcf
updated 10 months ago by
Ram
43k • written 11.1 years ago by
Erik Garrison
★ 2.4k
38
votes
21
replies
19k
views
8 follow
Tool:
pybam - 100% python BAM reader
python
htspython
bam
pysam
updated 10 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 10 months ago by
Ram
43k • written 6.9 years ago by
bernatgel
★ 3.4k
0
votes
0
replies
420
views
Tool:
Announcing the Papilloma Virus Episteme (PaVE) 2.0 Release
genomics
HPV
3D
2.0 years ago by
karlynn.noble
▴ 60
0
votes
0
replies
397
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
2.0 years ago by
Michael
54k
733 results • Page
2 of 15
Recent Votes
Answer: Searching for gene in multiple genomes
Comment: RNA velocity for smart-seq2 dataset
Answer: RNA velocity for smart-seq2 dataset
Answer: RNA velocity for smart-seq2 dataset
Comment: Help with choosing a model species for Augustus for a de novo assembled genome.
A: After read mapping, count exons or genes?
After read mapping, count exons or genes?
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SHN
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Recent Replies
Comment: creating batch colum for batch correction
by
ATpoint
82k
Not sure I follow. Can you first of all describe which comparisons you want to make, pretending there was no batch effect at all. Write dow…
Comment: Pindel Segmentation Fault Error
by
Ruqaiya
• 0
This the tool still problematic?
Comment: Segmentation error while using a tool
by
Ruqaiya
• 0
Thank you for the advice, i'll keep that in mind.
Comment: Segmentation error while using a tool
by
Ruqaiya
• 0
I am trying to reproduce some bioinformatics data from a research paper-[this paper][1] as i was asked to work on an MRSA bioinfo project, …
Answer: Segmentation error while using a tool
by
Mensur Dlakic
★ 27k
Most likely you didn't do anything wrong. Going by your previous post that you have only 8 GB of RAM, the most likely reason is the lack of…
Comment: Segmentation error while using a tool
by
Thanujay S
• 0
Hey @Ruqaiya! Can you please give more details on why smalt is opted here? According to what I can see, the tool has become obsolete! Why …
Comment: Extracting mutation status from MAF files - TCGA
by
Thanujay S
• 0
Hey! Can you explain the question further? What have you tried?
Comment: Downloading older version of a tool
by
Ruqaiya
• 0
I tried the 2nd option only. I got the files of older version from the author but that version isn't working on my WSL, it's showing Segmen…
Comment: filtering before dada2
by
GenoMax
142k
> I encountered a significant decrease in the percentage of merged reads. You can check with `bbmerge.sh` from BBMap suite to see how many…
Comment: HCL database download
by
GenoMax
142k
Isn't the download link available above the plot: http://bis.zju.edu.cn/HCL/data/DGE/Adult-Transverse-Colon1_dge.txt.gz
Comment: fastq screen aligner no specified.
by
GenoMax
142k
You need to change this configuration file to point it to the location where the aligner executable can be found. So as an example followi…
Answer: Design matrix Differential expression analysis
by
Gordon Smyth
★ 7.1k
The expression levels do not change but the way that you have parametrized the expression levels does change. The two design matrices give…
Comment: The GDC Legacy Archive is retiring soon.
by
lcordeiro
▴ 40
Hi Zhenyu, do you happen to know how I can download metadata for some of the legacy files? I downloaded several IDATs from the legacy data …
Answer: Force PLINK2 to neglect chrX as the sex chromosome
by
chrchang523
10k
(cross-posted from https://groups.google.com/g/plink2-users/c/Qphx_6BpPII ) You need to use --chr-set, not --allow-extra-chr, to specify…
Answer: Easy way to find out which allele is minor allele from bed file?
by
chrchang523
10k
This question does not make sense. If you care about allele-order "information [being] lost in downstream applications", REF/ALT is the ob…
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