Owner

lpantano

12 indexed repositories · View on GitHub

seqcluster
small RNA analysis from NGS data

HTML · 39 stars
DEGreport
Create a cromphensive report of DEG list coming from any analysis of RNAseq data

R · 30 stars
seqbuster
pipeline for the analysis of small RNA data

Java · 14 stars
isomiRs
analyze isomiRs from seqbuster tool

R · 8 stars
seqclusterViz
visualization of seqcluster output, try at:

JavaScript · 6 stars
bcbioSmallRna
R package to analyze data after small RNAseq with bcbio

HTML · 6 stars
bcbio.coverage
utils functions for exome coverage plots as quality controls

Python · 4 stars
seqcluster-helper
Help for the installation and configuration of seqcluster tool

Python · 2 stars
eggs
new ideas that may fails or success about bioinformatics

HTML · 2 stars
mirdeep2_core
Main core scripts for novel mirna discovery from bam files

Perl · 0 stars
cambridge-bio-developer-ladies
material we talk in our meet-ups

HTML · 0 stars
myself
source code from my personal web page

Astro · 0 stars

Beginner friendly Everything

Open All

degCovariates has inconsistent documentation Open

Difficulty 3/5 1-2 days Newbie friendliness 52/100

lpantano/DEGreport#70 · 1 comment · Opened Jul 19, 2026
[Scientists] A Lab-Scale Pipeline Factory: Agentic Infrastructure for Nextflow Development Open

audience:scientists stage:social-media-ready

Difficulty 3/5 1-2 days Newbie friendliness 52/100

lpantano/myself#82 · 1 comment · Opened May 1, 2026
About isoPlot function Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

lpantano/isomiRs#32 · Opened Jan 25, 2026
[General Public] Why 60% of Us Share Misleading Data Without Knowing Open

audience:general-public stage:backlog

Difficulty 4/5 3-5 days Newbie friendliness 38/100

lpantano/myself#68 · Opened Jan 10, 2026
[General Public] COVID Charts: Why 84% of Misleading Posts Werent Bad Charts Open

audience:general-public stage:backlog

Difficulty 4/5 3-5 days Newbie friendliness 30/100

lpantano/myself#67 · Opened Jan 10, 2026
[General Public] They Dont Make Them Like They Used To (Or Do They?) Open

audience:general-public stage:backlog

Difficulty 3/5 1-2 days Newbie friendliness 55/100

lpantano/myself#66 · Opened Jan 10, 2026
[General Public] Mutual Fund Survivor Stories: The Funds You Never Hear About Open

audience:general-public stage:backlog

Difficulty 3/5 1-2 days Newbie friendliness 45/100

lpantano/myself#65 · Opened Jan 10, 2026
[General Public] When Health Apps Claim Medical-Grade Accuracy Open

audience:general-public stage:backlog

Difficulty 3/5 1-2 days Newbie friendliness 55/100

lpantano/myself#64 · Opened Jan 10, 2026
[General Public] What Your Sleep Tracker Gets Wrong (And Right) Open

audience:general-public stage:backlog

Difficulty 3/5 1-2 days Newbie friendliness 45/100

lpantano/myself#62 · Opened Jan 10, 2026
[General Public] How Misleading Graphs Trick Your Brain Open

audience:general-public stage:backlog

Difficulty 4/5 3-5 days Newbie friendliness 35/100

lpantano/myself#61 · Opened Jan 10, 2026
[General Public] Survivorship Bias: The Hidden Data in Your Daily Decisions Open

audience:general-public stage:backlog

Difficulty 3/5 1-2 days Newbie friendliness 55/100

lpantano/myself#60 · Opened Jan 10, 2026
[General Public] Health Data Transparency: What You Deserve to Know Open

audience:general-public priority:high stage:backlog

Difficulty 4/5 3-5 days Newbie friendliness 35/100

lpantano/myself#59 · Opened Jan 10, 2026
[Scientists] Data Management Plans That Actually Work Open

audience:scientists stage:backlog

Difficulty 4/5 3-5 days Newbie friendliness 35/100

lpantano/myself#58 · Opened Jan 10, 2026
[Scientists] AiiDA for Computational Provenance Tracking Open

audience:scientists stage:backlog

Difficulty 4/5 3-5 days Newbie friendliness 35/100

lpantano/myself#56 · Opened Jan 10, 2026
[Scientists] Breaking Down Departmental Data Silos Open

audience:scientists stage:backlog

Difficulty 5/5 Over a week Newbie friendliness 35/100

lpantano/myself#55 · Opened Jan 10, 2026
[Scientists] Version Control for Data Science: Beyond Git Basics Open

audience:scientists stage:backlog

Difficulty 4/5 3-5 days Newbie friendliness 45/100

lpantano/myself#54 · Opened Jan 10, 2026
[Scientists] Nextflow Pipeline Best Practices for Production Open

audience:scientists stage:backlog

Difficulty 5/5 Over a week Newbie friendliness 25/100

lpantano/myself#53 · Opened Jan 10, 2026
[Scientists] AI Tools for Literature Review: Elicit, Consensus, and Beyond Open

audience:scientists stage:backlog

Difficulty 4/5 3-5 days Newbie friendliness 35/100

lpantano/myself#52 · 1 comment · Opened Jan 10, 2026
[Scientists] Reproducible Research with Docker Containers Open

audience:scientists stage:backlog

Difficulty 4/5 3-5 days Newbie friendliness 42/100

lpantano/myself#51 · Opened Jan 10, 2026
[Scientists] Spec-Driven Development: Upgrading Claude.md with Spec-Kit Open

audience:scientists stage:backlog

Difficulty 3/5 1-2 days Newbie friendliness 35/100

lpantano/myself#50 · Opened Jan 10, 2026
[Scientists] Organizing Thousands of Samples in Google Cloud for Genomics Open

audience:scientists stage:backlog

Difficulty 4/5 3-5 days Newbie friendliness 35/100

lpantano/myself#48 · Opened Jan 10, 2026
[Scientists] DEGreport R Package: Mastering Gene Clustering with degPatterns Open

audience:scientists stage:backlog

Difficulty 4/5 3-5 days Newbie friendliness 35/100

lpantano/myself#47 · Opened Jan 10, 2026
degQC, ggplot2::labels Error Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

lpantano/DEGreport#69 · 1 comment · Opened Oct 17, 2025
add abrf2025 Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

lpantano/myself#38 · Opened May 4, 2025
About IsoNetwork Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

lpantano/isomiRs#31 · 1 comment · Opened Nov 3, 2024
Mirtopfiles can not load with IsomirDataSeqFromMirtop Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

lpantano/isomiRs#30 · 7 comments · Opened Nov 1, 2024
Connecting dots and lines in degPlotCluster() Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

lpantano/DEGreport#66 · 1 comment · Opened Aug 30, 2024
New genes that did not exist in dds object suddenly showed up after degPatterns Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

lpantano/DEGreport#65 · 1 comment · Opened Mar 28, 2024
Clarification with degMerge function Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

lpantano/DEGreport#64 · 1 comment · Opened Mar 27, 2024
Is there a license? Open

Difficulty 1/5 Under an hour Newbie friendliness 65/100

lpantano/seqbuster#27 · Opened Feb 22, 2024
`isomiR` annotation Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

lpantano/isomiRs#29 · 1 comment · 1 reaction · Opened Jan 4, 2024
Percent abundance in `isoPlot` Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

lpantano/isomiRs#28 · 2 reactions · Opened Jan 2, 2024
`.collapse_mirs` function is not used anywhere Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

lpantano/isomiRs#27 · 1 reaction · Opened Dec 7, 2023
`isoNorm` applies a different normalization function Open

Difficulty 2/5 1-3 hours Newbie friendliness 56/100

lpantano/isomiRs#26 · 1 reaction · Opened Dec 7, 2023
`isoCounts` for `seed=TRUE` is void Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

lpantano/isomiRs#25 · 1 reaction · Opened Dec 7, 2023
`isoCounts` for different isomiR types Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

lpantano/isomiRs#23 · 2 comments · 1 reaction · Opened Dec 5, 2023
An error occurred when running the program Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

lpantano/seqcluster#56 · 4 comments · Opened Nov 8, 2023
possible error with pandas 1.1 Open

Difficulty 3/5 1-2 days Newbie friendliness 20/100

lpantano/seqcluster#51 · Opened Sep 2, 2020
isoAnnotate error Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

lpantano/isomiRs#18 · 13 comments · 1 reaction · Opened Aug 12, 2020
Bioconda -> Github is wrong link Open

Difficulty 1/5 Under an hour Newbie friendliness 55/100

lpantano/seqcluster#50 · Opened Aug 1, 2020
`degCovariates`: breaking change in dplyr filter code Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

lpantano/DEGreport#36 · 6 comments · Opened Jun 26, 2020
How to re-cluster in each group for DEGpattern? Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

lpantano/DEGreport#35 · 1 reaction · Opened Jun 24, 2020
Can we order the top N genes within degplot Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

lpantano/DEGreport#33 · 5 comments · Opened May 30, 2020
input only 2~3 isomiRs / missing mismatch for 3'trim variation Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

lpantano/isomiRs#17 · 7 comments · Opened Apr 25, 2020
degCovariates ERROR Open

Difficulty 3/5 1-2 days Newbie friendliness 28/100

lpantano/DEGreport#32 · 1 comment · Opened Apr 17, 2020
input error with mirtop export file Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

lpantano/isomiRs#16 · 5 comments · Opened Apr 17, 2020
error message Open

Difficulty 4/5 3-5 days Newbie friendliness 18/100

lpantano/DEGreport#30 · 1 comment · Opened Mar 31, 2020
Cannot upload bcbio run Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

lpantano/bcbioSmallRna#3 · 1 comment · Opened Feb 23, 2020
Add prefix to the title plot Open

Difficulty 2/5 1-3 hours Newbie friendliness 58/100

lpantano/DEGreport#29 · Opened Jan 7, 2020
degPatterns results exists unsimilar pattern in a cluster Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

lpantano/DEGreport#28 · 1 comment · Opened Aug 25, 2019

lpantano

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